From: Peter Amstutz Date: Tue, 18 Aug 2020 18:12:43 +0000 (-0400) Subject: 15964: Batch change qr1hi->zzzzz X-Git-Tag: 2.1.0~108^2~5 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/dba9e46d852b50d2d72bd9619667f69637370fd7 15964: Batch change qr1hi->zzzzz Change some uuids to point to new collections on pirca Delete several unlinked, obsolete crunch1 documentation pages. Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml b/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml index 73bd9f599c..4920bb29ea 100755 --- a/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml +++ b/doc/user/cwl/bwa-mem/bwa-mem-input-mixed.yml @@ -15,15 +15,15 @@ cwl:tool: bwa-mem.cwl reference: class: File location: keep:2463fa9efeb75e099685528b3b9071e0+438/19.fasta.bwt - arv:collectionUUID: qr1hi-4zz18-pwid4w22a40jp8l + arv:collectionUUID: pirca-4zz18-jyjuzyqq14qspl7 read_p1: class: File location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_1.fastq - arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0 + arv:collectionUUID: pirca-4zz18-fhbq692jyemnknq read_p2: class: File location: keep:ae480c5099b81e17267b7445e35b4bc7+180/HWI-ST1027_129_D0THKACXX.1_2.fastq - arv:collectionUUID: qr1hi-4zz18-h615rgfmqt3wje0 + arv:collectionUUID: pirca-4zz18-fhbq692jyemnknq group_id: arvados_tutorial sample_id: HWI-ST1027_129 PL: illumina diff --git a/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml b/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml index 7e71e959eb..736a58beb0 100755 --- a/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml +++ b/doc/user/cwl/bwa-mem/bwa-mem-input-uuids.yml @@ -9,13 +9,13 @@ cwl:tool: bwa-mem.cwl reference: class: File - location: keep:qr1hi-4zz18-pwid4w22a40jp8l/19.fasta.bwt + location: keep:pirca-4zz18-jyjuzyqq14qspl7/19.fasta.bwt read_p1: class: File - location: keep:qr1hi-4zz18-h615rgfmqt3wje0/HWI-ST1027_129_D0THKACXX.1_1.fastq + location: keep:pirca-4zz18-fhbq692jyemnknq/HWI-ST1027_129_D0THKACXX.1_1.fastq read_p2: class: File - location: keep:qr1hi-4zz18-h615rgfmqt3wje0/HWI-ST1027_129_D0THKACXX.1_2.fastq + location: keep:pirca-4zz18-fhbq692jyemnknq/HWI-ST1027_129_D0THKACXX.1_2.fastq group_id: arvados_tutorial sample_id: HWI-ST1027_129 PL: illumina diff --git a/doc/user/cwl/bwa-mem/bwa-mem.cwl b/doc/user/cwl/bwa-mem/bwa-mem.cwl index 2001971264..a73329288c 100755 --- a/doc/user/cwl/bwa-mem/bwa-mem.cwl +++ b/doc/user/cwl/bwa-mem/bwa-mem.cwl @@ -8,7 +8,7 @@ class: CommandLineTool hints: DockerRequirement: - dockerPull: lh3lh3/bwa + dockerPull: quay.io/biocontainers/bwa:0.7.17--ha92aebf_3 baseCommand: [mem] diff --git a/doc/user/cwl/cwl-run-options.html.textile.liquid b/doc/user/cwl/cwl-run-options.html.textile.liquid index 725528f44d..0c7de5cb3a 100644 --- a/doc/user/cwl/cwl-run-options.html.textile.liquid +++ b/doc/user/cwl/cwl-run-options.html.textile.liquid @@ -74,10 +74,10 @@ Use the @--name@ and @--output-name@ options to specify the name of the workflow 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --name "Example bwa run" --output-name "Example bwa output" bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
@@ -98,9 +98,9 @@ To submit a workflow and exit immediately, use the @--no-wait@ option.  This wil
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --no-wait bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Uploaded to qr1hi-4zz18-eqnfwrow8aysa9q
-2016-06-30 15:07:52 arvados.cwl-runner[12480] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-qr1hi-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 15:07:52 arvados.arv-run[12480] INFO: Uploaded to zzzzz-4zz18-eqnfwrow8aysa9q
+2016-06-30 15:07:52 arvados.cwl-runner[12480] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+zzzzz-8i9sb-fm2n3b1w0l6bskg
 

 
 
@@ -111,10 +111,10 @@ To run a workflow with local control, use @--local@.  This means that the host w
 
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --local bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance qr1hi-d1hrv-92wcu6ldtio74r4
-2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Queued
-2016-07-01 10:05:29 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Running
-2016-07-01 10:05:45 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-2nzzfbuf9zjrj4g) is Complete
+2016-07-01 10:05:19 arvados.cwl-runner[16290] INFO: Pipeline instance zzzzz-d1hrv-92wcu6ldtio74r4
+2016-07-01 10:05:28 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-2nzzfbuf9zjrj4g) is Queued
+2016-07-01 10:05:29 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-2nzzfbuf9zjrj4g) is Running
+2016-07-01 10:05:45 arvados.cwl-runner[16290] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-2nzzfbuf9zjrj4g) is Complete
 2016-07-01 10:05:46 arvados.cwl-runner[16290] INFO: Overall process status is success
 {
     "aligned_sam": {
diff --git a/doc/user/cwl/cwl-runner.html.textile.liquid b/doc/user/cwl/cwl-runner.html.textile.liquid
index 8af1c574f5..3ed26a0071 100644
--- a/doc/user/cwl/cwl-runner.html.textile.liquid
+++ b/doc/user/cwl/cwl-runner.html.textile.liquid
@@ -19,30 +19,27 @@ h2. Running arvados-cwl-runner
 
 h3. Get the example files
 
-The tutorial files are located in the "documentation section of the Arvados source repository:":https://github.com/arvados/arvados/tree/master/doc/user/cwl/bwa-mem
+The tutorial files are located in the documentation section of the Arvados source repository, which can be found on "git.arvados.org": https://git.arvados.org/arvados.git/tree/HEAD:/doc/user/cwl/bwa-mem or "github":https://github.com/arvados/arvados/tree/master/doc/user/cwl/bwa-mem
 
 
-
~$ git clone https://github.com/arvados/arvados
+
~$ git clone https://git.arvados.org/arvados.git
 ~$ cd arvados/doc/user/cwl/bwa-mem
 

 
 
-The tutorial data is hosted on "https://playground.arvados.org":https://playground.arvados.org (also referred to by the identifier *qr1hi*).  If you are using a different Arvados instance, you may need to copy the data to your own instance.  The easiest way to do this is with "arv-copy":{{site.baseurl}}/user/topics/arv-copy.html (this requires signing up for a free playground.arvados.org account).
+The tutorial data is hosted on "https://playground.arvados.org":https://playground.arvados.org (also referred to by the identifier *pirca*).  If you are using a different Arvados instance, you may need to copy the data to your own instance.  One way to do this is with "arv-copy":{{site.baseurl}}/user/topics/arv-copy.html (this requires signing up for a free playground.arvados.org account).
 
 
-
~$ arv-copy --src qr1hi --dst settings 2463fa9efeb75e099685528b3b9071e0+438
-~$ arv-copy --src qr1hi --dst settings ae480c5099b81e17267b7445e35b4bc7+180
-~$ arv-copy --src qr1hi --dst settings 655c6cd07550151b210961ed1d3852cf+57
+
~$ arv-copy --src pirca --dst settings 2463fa9efeb75e099685528b3b9071e0+438
+~$ arv-copy --src pirca --dst settings ae480c5099b81e17267b7445e35b4bc7+180
 

 
 
 If you do not wish to create an account on "https://playground.arvados.org":https://playground.arvados.org, you may download the files anonymously and upload them to your local Arvados instance:
 
-"https://playground.arvados.org/collections/2463fa9efeb75e099685528b3b9071e0+438":https://playground.arvados.org/collections/2463fa9efeb75e099685528b3b9071e0+438
+"https://collections.pirca.arvadosapi.com/c=2463fa9efeb75e099685528b3b9071e0+438/":https://collections.pirca.arvadosapi.com/c=2463fa9efeb75e099685528b3b9071e0+438/
 
-"https://playground.arvados.org/collections/ae480c5099b81e17267b7445e35b4bc7+180":https://playground.arvados.org/collections/ae480c5099b81e17267b7445e35b4bc7+180
-
-"https://playground.arvados.org/collections/655c6cd07550151b210961ed1d3852cf+57":https://playground.arvados.org/collections/655c6cd07550151b210961ed1d3852cf+57
+"https://collections.pirca.arvadosapi.com/c=ae480c5099b81e17267b7445e35b4bc7+180/":https://collections.pirca.arvadosapi.com/c=ae480c5099b81e17267b7445e35b4bc7+180/
 
 h2. Submitting a workflow to an Arvados cluster
 
@@ -56,10 +53,10 @@ Use @arvados-cwl-runner@ to submit CWL workflows to Arvados.  After submitting t
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
@@ -87,10 +84,10 @@ You can also execute CWL files directly from Keep:
 
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner keep:655c6cd07550151b210961ed1d3852cf+57/bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
diff --git a/doc/user/getting_started/check-environment.html.textile.liquid b/doc/user/getting_started/check-environment.html.textile.liquid
index b707891a1e..1097e4e9d8 100644
--- a/doc/user/getting_started/check-environment.html.textile.liquid
+++ b/doc/user/getting_started/check-environment.html.textile.liquid
@@ -16,14 +16,14 @@ Check that you are able to access the Arvados API server using @arv user current
 
 
$ arv user current
 {
- "href":"https://qr1hi.arvadosapi.com/arvados/v1/users/qr1hi-xioed-9z2p3pn12yqdaem",
+ "href":"https://zzzzz.arvadosapi.com/arvados/v1/users/zzzzz-xioed-9z2p3pn12yqdaem",
  "kind":"arvados#user",
  "etag":"8u0xwb9f3otb2xx9hto4wyo03",
- "uuid":"qr1hi-tpzed-92d3kxnimy3d4e8",
- "owner_uuid":"qr1hi-tpqed-23iddeohxta2r59",
+ "uuid":"zzzzz-tpzed-92d3kxnimy3d4e8",
+ "owner_uuid":"zzzzz-tpqed-23iddeohxta2r59",
  "created_at":"2013-12-02T17:05:47Z",
- "modified_by_client_uuid":"qr1hi-xxfg8-owxa2oa2s33jyej",
- "modified_by_user_uuid":"qr1hi-tpqed-23iddeohxta2r59",
+ "modified_by_client_uuid":"zzzzz-xxfg8-owxa2oa2s33jyej",
+ "modified_by_user_uuid":"zzzzz-tpqed-23iddeohxta2r59",
  "modified_at":"2013-12-02T17:07:08Z",
  "updated_at":"2013-12-05T19:51:08Z",
  "email":"you@example.com",
diff --git a/doc/user/topics/arv-copy.html.textile.liquid b/doc/user/topics/arv-copy.html.textile.liquid
index 805d71b2df..e5e631d4e2 100644
--- a/doc/user/topics/arv-copy.html.textile.liquid
+++ b/doc/user/topics/arv-copy.html.textile.liquid
@@ -17,54 +17,54 @@ h2. arv-copy
 
 @arv-copy@ allows users to copy collections and workflows from one cluster to another. By default, @arv-copy@ will recursively go through the workflow and copy all dependencies associated with the object.
 
-For example, let's copy from the Arvados playground, also known as *qr1hi*, to *dst_cluster*. The names *qr1hi* and *dst_cluster* are interchangable with any cluster name. You can find the cluster name from the prefix of the uuid of the object you want to copy. For example, in *qr1hi*-4zz18-tci4vn4fa95w0zx, the cluster name is qr1hi.
+For example, let's copy from the Arvados playground, also known as *pirca*, to *dstcl*. The names *pirca* and *dstcl* are interchangable with any cluster id. You can find the cluster name from the prefix of the uuid of the object you want to copy. For example, in *zzzzz*-4zz18-tci4vn4fa95w0zx, the cluster name is zzzzz.
 
-In order to communicate with both clusters, you must create custom configuration files for each cluster. In the Arvados Workbench, click on the dropdown menu icon   in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Current token*. Copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ in both of your clusters. Then, create two configuration files, one for each cluster. The names of the files must have the format of *ClusterID.conf*. In our example, let's make two files, one for *qr1hi* and one for *dst_cluster*. From your *Current token* page in *qr1hi* and *dst_cluster*, copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@.
+In order to communicate with both clusters, you must create custom configuration files for each cluster. In the Arvados Workbench, click on the dropdown menu icon   in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Current token*. Copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ in both of your clusters. Then, create two configuration files, one for each cluster. The names of the files must have the format of *ClusterID.conf*. In our example, let's make two files, one for *pirca* and one for *dstcl*. From your *Current token* page in *pirca* and *dstcl*, copy the @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@.
 
 !{display: block;margin-left: 25px;margin-right: auto;}{{ site.baseurl }}/images/api-token-host.png!
 
-Copy your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ into the config files as shown below in the shell account from which you are executing the commands. For example, the default shell you may have access to is shell.qr1hi. You can add these files in ~/.config/arvados/ in the qr1hi shell terminal.
+Copy your @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ into the config files as shown below in the shell account from which you are executing the commands. For example, the default shell you may have access to is shell.pirca. You can add these files in ~/.config/arvados/ in the pirca shell terminal.
 
 
 
~$ cd ~/.config/arvados
-~$ echo "ARVADOS_API_HOST=qr1hi.arvadosapi.com" >> qr1hi.conf
-~$ echo "ARVADOS_API_TOKEN=123456789abcdefghijkl" >> qr1hi.conf
-~$ echo "ARVADOS_API_HOST=dst_cluster.arvadosapi.com" >> dst_cluster.conf
-~$ echo "ARVADOS_API_TOKEN=987654321lkjihgfedcba" >> dst_cluster.conf
+~$ echo "ARVADOS_API_HOST=pirca.arvadosapi.com" >> pirca.conf
+~$ echo "ARVADOS_API_TOKEN=123456789abcdefghijkl" >> pirca.conf
+~$ echo "ARVADOS_API_HOST=dstcl.arvadosapi.com" >> dstcl.conf
+~$ echo "ARVADOS_API_TOKEN=987654321lkjihgfedcba" >> dstcl.conf
 

 
 
-Now you're ready to copy between *qr1hi* and *dst_cluster*!
+Now you're ready to copy between *pirca* and *dstcl*!
 
 h3. How to copy a collection
 
 First, select the uuid of the collection you want to copy from the source cluster. The uuid can be found in the collection display page in the collection summary area (top left box), or from the URL bar (the part after @collections/...@)
 
-Now copy the collection from *qr1hi* to *dst_cluster*. We will use the uuid @qr1hi-4zz18-tci4vn4fa95w0zx@ as an example. You can find this collection in the lobSTR v.3 project on playground.arvados.org.
+Now copy the collection from *pirca* to *dstcl*. We will use the uuid @pirca-4zz18-jyjuzyqq14qspl7@ as an example. You can find this collection in the User guide resources project on playground.arvados.org.
 
-
~$ arv-copy --src qr1hi --dst dst_cluster qr1hi-4zz18-tci4vn4fa95w0zx
-qr1hi-4zz18-tci4vn4fa95w0zx: 6.1M / 6.1M 100.0%
-arvados.arv-copy[1234] INFO: Success: created copy with uuid dst_cluster-4zz18-8765943210cdbae
+
~$ arv-copy --src pirca --dst dstcl pirca-4zz18-jyjuzyqq14qspl7
+pirca-4zz18-tci4vn4fa95w0zx: 6.1M / 6.1M 100.0%
+arvados.arv-copy[1234] INFO: Success: created copy with uuid dstcl-4zz18-8765943210cdbae
 

 
 
 The output of arv-copy displays the uuid of the collection generated in the destination cluster. By default, the output is placed in your home project in the destination cluster. If you want to place your collection in a pre-created project, you can specify the project you want it to be in using the tag @--project-uuid@ followed by the project uuid.
 
-For example, this will copy the collection to project dst_cluster-j7d0g-a894213ukjhal12 in the destination cluster.
+For example, this will copy the collection to project dstcl-j7d0g-a894213ukjhal12 in the destination cluster.
 
- 
~$ arv-copy --src qr1hi --dst dst_cluster --project-uuid dst_cluster-j7d0g-a894213ukjhal12 qr1hi-4zz18-tci4vn4fa95w0zx
+ 
~$ arv-copy --src pirca --dst dstcl --project-uuid dstcl-j7d0g-a894213ukjhal12 pirca-4zz18-tci4vn4fa95w0zx
 

 
 
 h3. How to copy a workflow
 
-We will use the uuid @zzzzz-7fd4e-sampleworkflow1@ as an example workflow.
+We will use the uuid @pirca-7fd4e-sampleworkflow1@ as an example workflow.
 
 
-
~$ arv-copy --src zzzzz --dst dst_cluster --dst-git-repo $USER/tutorial zzzzz-7fd4e-sampleworkflow1
-zzzzz-4zz18-jidprdejysravcr: 1143M / 1143M 100.0%
+
~$ arv-copy --src pirca --dst dstcl --dst-git-repo $USER/tutorial pirca-7fd4e-sampleworkflow1
+pirca-4zz18-jidprdejysravcr: 1143M / 1143M 100.0%
 2017-01-04 04:11:58 arvados.arv-copy[5906] INFO:
-2017-01-04 04:11:58 arvados.arv-copy[5906] INFO: Success: created copy with uuid dst_cluster-7fd4e-ojtgpne594ubkt7
+2017-01-04 04:11:58 arvados.arv-copy[5906] INFO: Success: created copy with uuid dstcl-7fd4e-ojtgpne594ubkt7
 

 
 
@@ -75,6 +75,6 @@ If you would like to copy the object without dependencies, you can use the @--no
 For example, we can copy the same object non-recursively using the following:
 
 
-
~$ arv-copy --src zzzzz --dst dst_cluster --dst-git-repo $USER/tutorial --no-recursive zzzzz-7fd4e-sampleworkflow1
+
~$ arv-copy --src pirca --dst dstcl --dst-git-repo $USER/tutorial --no-recursive pirca-7fd4e-sampleworkflow1
 

 
diff --git a/doc/user/topics/arv-docker.html.textile.liquid b/doc/user/topics/arv-docker.html.textile.liquid
index d371400f5c..b03ef0bdf1 100644
--- a/doc/user/topics/arv-docker.html.textile.liquid
+++ b/doc/user/topics/arv-docker.html.textile.liquid
@@ -103,7 +103,7 @@ h3. Uploading Docker images to a shared project
 Docker images are subject to normal Arvados permissions.  If wish to share your Docker image with others you should use @arv-keepdocker@ with the @--project-uuid@ option to add the image to a shared project and ensure that metadata is set correctly.
 
 
-
$ arv-keepdocker docker-example-r-base --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx
+
$ arv-keepdocker docker-example-r-base --project-uuid zzzzz-j7d0g-xxxxxxxxxxxxxxx
 

 
 
diff --git a/doc/user/topics/arv-web.html.textile.liquid b/doc/user/topics/arv-web.html.textile.liquid
deleted file mode 100644
index 9671e97096..0000000000
--- a/doc/user/topics/arv-web.html.textile.liquid
+++ /dev/null
@@ -1,106 +0,0 @@
----
-layout: default
-navsection: userguide
-title: "Using arv-web"
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-@arv-web@ enables you to run a custom web service from the contents of an Arvados collection.
-
-{% include 'tutorial_expectations_workstation' %}
-
-h2. Usage
-
-@arv-web@ enables you to set up a web service based on the most recent collection in a project.  An arv-web application is a reproducible, immutable application bundle where the web app is packaged with both the code to run and the data to serve.  Because Arvados Collections can be updated with minimum duplication, it is efficient to produce a new application bundle when the code or data needs to be updated; retaining old application bundles makes it easy to go back and run older versions of your web app.
-
-
-$ cd $HOME/arvados/services/arv-web
-usage: arv-web.py [-h] --project-uuid PROJECT_UUID [--port PORT]
-                  [--image IMAGE]
-
-optional arguments:
-  -h, --help            show this help message and exit
-  --project-uuid PROJECT_UUID
-                        Project uuid to watch
-  --port PORT           Host port to listen on (default 8080)
-  --image IMAGE         Docker image to run
-

-
-At startup, @arv-web@ queries an Arvados project and mounts the most recently modified collection into a temporary directory.  It then runs a Docker image with the collection bound to @/mnt@ inside the container.  When a new collection is added to the project, or an existing project is updated, it will stop the running Docker container, unmount the old collection, mount the new most recently modified collection, and restart the Docker container with the new mount.
-
-h2. Docker container
-
-The @Dockerfile@ in @arvados/docker/arv-web@ builds a Docker image that runs Apache with @/mnt@ as the DocumentRoot.  It is configured to run web applications which use Python WSGI, Ruby Rack, or CGI; to serve static HTML; or browse the contents of the @public@ subdirectory of the collection using default Apache index pages.
-
-To build the Docker image:
-
-
-
~$ cd arvados/docker
-~/arvados/docker$ docker build -t arvados/arv-web arv-web
-

-
-
-h2. Running sample applications
-
-First, in Arvados Workbench, create a new project.  Copy the project UUID from the URL bar (this is the part of the URL after @projects/...@).
-
-Now upload a collection containing a "Python WSGI web app:":http://wsgi.readthedocs.org/en/latest/
-
-
-
~$ cd arvados/services/arv-web
-~/arvados/services/arv-web$ arv-put --project [zzzzz-j7d0g-yourprojectuuid] --name sample-wsgi-app sample-wsgi-app
-0M / 0M 100.0%
-Collection saved as 'sample-wsgi-app'
-zzzzz-4zz18-ebohzfbzh82qmqy
-~/arvados/services/arv-web$ ./arv-web.py --project [zzzzz-j7d0g-yourprojectuuid] --port 8888
-2015-01-30 11:21:00 arvados.arv-web[4897] INFO: Mounting zzzzz-4zz18-ebohzfbzh82qmqy
-2015-01-30 11:21:01 arvados.arv-web[4897] INFO: Starting Docker container arvados/arv-web
-2015-01-30 11:21:02 arvados.arv-web[4897] INFO: Container id e79e70558d585a3e038e4bfbc97e5c511f21b6101443b29a8017bdf3d84689a3
-2015-01-30 11:21:03 arvados.arv-web[4897] INFO: Waiting for events
-

-
-
-The sample application will be available at @http://localhost:8888@.
-
-h3. Updating the application
-
-If you upload a new collection to the same project, arv-web will restart the web service and serve the new collection.  For example, uploading a collection containing a "Ruby Rack web app:":https://github.com/rack/rack/wiki
-
-
-
~$ cd arvados/services/arv-web
-~/arvados/services/arv-web$ arv-put --project [zzzzz-j7d0g-yourprojectuuid] --name sample-rack-app sample-rack-app
-0M / 0M 100.0%
-Collection saved as 'sample-rack-app'
-zzzzz-4zz18-dhhm0ay8k8cqkvg
-

-
-
-@arv-web@ will automatically notice the change, load a new container, and send an update signal (SIGHUP) to the service:
-
-
-2015-01-30 11:21:03 arvados.arv-web[4897] INFO:Waiting for events
-2015-01-30 11:21:04 arvados.arv-web[4897] INFO:create zzzzz-4zz18-dhhm0ay8k8cqkvg
-2015-01-30 11:21:05 arvados.arv-web[4897] INFO:Mounting zzzzz-4zz18-dhhm0ay8k8cqkvg
-2015-01-30 11:21:06 arvados.arv-web[4897] INFO:Sending refresh signal to container
-2015-01-30 11:21:07 arvados.arv-web[4897] INFO:Waiting for events
-

-
-h2. Writing your own applications
-
-The @arvados/arv-web@ image serves Python and Ruby applications using Phusion Passenger and Apache @mod_passenger@.  See "Phusion Passenger users guide for Apache":https://www.phusionpassenger.com/documentation/Users%20guide%20Apache.html for details, and look at the sample apps @arvados/services/arv-web/sample-wsgi-app@ and @arvados/services/arv-web/sample-rack-app@.
-
-You can serve CGI applications using standard Apache CGI support.  See "Apache Tutorial: Dynamic Content with CGI":https://httpd.apache.org/docs/current/howto/cgi.html for details, and look at the sample app @arvados/services/arv-web/sample-cgi-app@.
-
-You can also serve static content from the @public@ directory of the collection.  Look at @arvados/services/arv-web/sample-static-page@ for an example.  If no @index.html@ is found in @public/@, it will render default Apache index pages, permitting simple browsing of the collection contents.
-
-h3. Custom images
-
-You can provide your own Docker image.  The Docker image that will be used create the web application container is specified in the @docker_image@ file in the root of the collection.  You can also specify @--image@ on the command @arv-web@ line to choose the docker image (this will override the contents of @docker_image@).
-
-h3. Reloading the web service
-
-Stopping the Docker container and starting it again can result in a small amount of downtime.  When the collection containing a new or updated web application uses the same Docker image as the currently running web application, it is possible to avoid this downtime by keeping the existing container and only reloading the web server.  This is accomplished by providing a file called @reload@ in the root of the collection, which should contain the commands necessary to reload the web server inside the container.
diff --git a/doc/user/topics/keep.html.textile.liquid b/doc/user/topics/keep.html.textile.liquid
index 68b6a87d09..c415cebbdd 100644
--- a/doc/user/topics/keep.html.textile.liquid
+++ b/doc/user/topics/keep.html.textile.liquid
@@ -38,7 +38,7 @@ notextile. 
~$ cd /scratch/you
 
 When you run this command, you may get this API warning:
 
-notextile. 
WARNING:root:API lookup failed for collection 204e43b8a1185621ca55a94839582e6f+67108864 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://qr1hi.arvadosapi.com/arvados/v1/collections/204e43b8a1185621ca55a94839582e6f%2B67108864?alt=json returned "Not Found">)

+notextile. 
WARNING:root:API lookup failed for collection 204e43b8a1185621ca55a94839582e6f+67108864 (<class 'apiclient.errors.HttpError'>: <HttpError 404 when requesting https://zzzzz.arvadosapi.com/arvados/v1/collections/204e43b8a1185621ca55a94839582e6f%2B67108864?alt=json returned "Not Found">)

 
 This happens because @arv-get@ tries to find a collection with this identifier.  When that fails, it emits this warning, then looks for a datablock instead, which succeeds.
 
diff --git a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid b/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
deleted file mode 100644
index 544ccbd35e..0000000000
--- a/doc/user/topics/tutorial-gatk-variantfiltration.html.textile.liquid
+++ /dev/null
@@ -1,173 +0,0 @@
----
-layout: default
-navsection: userguide
-title: "Using GATK with Arvados"
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-This tutorial demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
-
-{% include 'tutorial_expectations' %}
-
-h2. Installing GATK
-
-Download the GATK binary tarball[1] -- e.g., @GenomeAnalysisTK-2.6-4.tar.bz2@ -- and "copy it to your Arvados VM":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
-
-
-
~$ arv-put GenomeAnalysisTK-2.6-4.tar.bz2
-c905c8d8443a9c44274d98b7c6cfaa32+94
-

-
-
-Next, you need the GATK Resource Bundle[2].  This may already be available in Arvados.  If not, you will need to download the files listed below and put them into Keep.
-
-
-
~$ arv keep ls -s d237a90bae3870b3b033aea1e99de4a9+10820
-  50342 1000G_omni2.5.b37.vcf.gz
-      1 1000G_omni2.5.b37.vcf.gz.md5
-    464 1000G_omni2.5.b37.vcf.idx.gz
-      1 1000G_omni2.5.b37.vcf.idx.gz.md5
-  43981 1000G_phase1.indels.b37.vcf.gz
-      1 1000G_phase1.indels.b37.vcf.gz.md5
-    326 1000G_phase1.indels.b37.vcf.idx.gz
-      1 1000G_phase1.indels.b37.vcf.idx.gz.md5
- 537210 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz
-      1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.gz.md5
-   3473 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz
-      1 CEUTrio.HiSeq.WGS.b37.bestPractices.phased.b37.vcf.idx.gz.md5
-  19403 Mills_and_1000G_gold_standard.indels.b37.vcf.gz
-      1 Mills_and_1000G_gold_standard.indels.b37.vcf.gz.md5
-    536 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz
-      1 Mills_and_1000G_gold_standard.indels.b37.vcf.idx.gz.md5
-  29291 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.gz.md5
-    565 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.sites.vcf.idx.gz.md5
-  37930 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.gz.md5
-    592 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf.idx.gz.md5
-5898484 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam
-    112 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.bai.gz.md5
-      1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam.md5
-   3837 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.gz.md5
-     65 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz
-      1 NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.vcf.idx.gz.md5
- 275757 dbsnp_137.b37.excluding_sites_after_129.vcf.gz
-      1 dbsnp_137.b37.excluding_sites_after_129.vcf.gz.md5
-   3735 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz
-      1 dbsnp_137.b37.excluding_sites_after_129.vcf.idx.gz.md5
- 998153 dbsnp_137.b37.vcf.gz
-      1 dbsnp_137.b37.vcf.gz.md5
-   3890 dbsnp_137.b37.vcf.idx.gz
-      1 dbsnp_137.b37.vcf.idx.gz.md5
-  58418 hapmap_3.3.b37.vcf.gz
-      1 hapmap_3.3.b37.vcf.gz.md5
-    999 hapmap_3.3.b37.vcf.idx.gz
-      1 hapmap_3.3.b37.vcf.idx.gz.md5
-      3 human_g1k_v37.dict.gz
-      1 human_g1k_v37.dict.gz.md5
-      2 human_g1k_v37.fasta.fai.gz
-      1 human_g1k_v37.fasta.fai.gz.md5
- 849537 human_g1k_v37.fasta.gz
-      1 human_g1k_v37.fasta.gz.md5
-      1 human_g1k_v37.stats.gz
-      1 human_g1k_v37.stats.gz.md5
-      3 human_g1k_v37_decoy.dict.gz
-      1 human_g1k_v37_decoy.dict.gz.md5
-      2 human_g1k_v37_decoy.fasta.fai.gz
-      1 human_g1k_v37_decoy.fasta.fai.gz.md5
- 858592 human_g1k_v37_decoy.fasta.gz
-      1 human_g1k_v37_decoy.fasta.gz.md5
-      1 human_g1k_v37_decoy.stats.gz
-      1 human_g1k_v37_decoy.stats.gz.md5
-

-
-
-h2. Submit a GATK job
-
-The Arvados distribution includes an example crunch script ("crunch_scripts/GATK2-VariantFiltration":https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/crunch_scripts/GATK2-VariantFiltration) that runs the GATK VariantFiltration tool with some default settings.
-
-
-
~$ src_version=76588bfc57f33ea1b36b82ca7187f465b73b4ca4
-~$ vcf_input=5ee633fe2569d2a42dd81b07490d5d13+82
-~$ gatk_binary=c905c8d8443a9c44274d98b7c6cfaa32+94
-~$ gatk_bundle=d237a90bae3870b3b033aea1e99de4a9+10820
-~$ cat >the_job <<EOF
-{
- "script":"GATK2-VariantFiltration",
- "repository":"arvados",
- "script_version":"$src_version",
- "script_parameters":
- {
-  "input":"$vcf_input",
-  "gatk_binary_tarball":"$gatk_binary",
-  "gatk_bundle":"$gatk_bundle"
- }
-}
-EOF
-

-
-
-* @"input"@ is collection containing the source VCF data. Here we are using an exome report from PGP participant hu34D5B9.
-* @"gatk_binary_tarball"@ is a Keep collection containing the GATK 2 binary distribution[1] tar file.
-* @"gatk_bundle"@ is a Keep collection containing the GATK resource bundle[2].
-
-Now start a job:
-
-
-
~$ arv job create --job "$(cat the_job)"
-{
- "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-n9k7qyp7bs5b9d4",
- "kind":"arvados#job",
- "etag":"9j99n1feoxw3az448f8ises12",
- "uuid":"qr1hi-8i9sb-n9k7qyp7bs5b9d4",
- "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "created_at":"2013-12-17T19:02:15Z",
- "modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
- "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "modified_at":"2013-12-17T19:02:15Z",
- "updated_at":"2013-12-17T19:02:15Z",
- "submit_id":null,
- "priority":null,
- "script":"GATK2-VariantFiltration",
- "script_parameters":{
-  "input":"5ee633fe2569d2a42dd81b07490d5d13+82",
-  "gatk_binary_tarball":"c905c8d8443a9c44274d98b7c6cfaa32+94",
-  "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820"
- },
- "script_version":"76588bfc57f33ea1b36b82ca7187f465b73b4ca4",
- "cancelled_at":null,
- "cancelled_by_client_uuid":null,
- "cancelled_by_user_uuid":null,
- "started_at":null,
- "finished_at":null,
- "output":null,
- "success":null,
- "running":null,
- "is_locked_by_uuid":null,
- "log":null,
- "runtime_constraints":{},
- "tasks_summary":{}
-}
-

-
-
-Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
-
-
~$ arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91
-hu34D5B9-exome-filtered.vcf
-

-
-
-h2. Notes
-
-fn1. "Download the GATK tools":http://www.broadinstitute.org/gatk/download
-
-fn2. "Information about the GATK resource bundle":http://gatkforums.broadinstitute.org/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it and "direct download link":ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/2.5/b37/ (if prompted, submit an empty password)
diff --git a/doc/user/topics/tutorial-job1.html.textile.liquid b/doc/user/topics/tutorial-job1.html.textile.liquid
deleted file mode 100644
index f7a2060101..0000000000
--- a/doc/user/topics/tutorial-job1.html.textile.liquid
+++ /dev/null
@@ -1,214 +0,0 @@
----
-layout: default
-navsection: userguide
-title: "Running a Crunch job on the command line"
-...
-{% comment %}
-Copyright (C) The Arvados Authors. All rights reserved.
-
-SPDX-License-Identifier: CC-BY-SA-3.0
-{% endcomment %}
-
-This tutorial introduces how to run individual Crunch jobs using the @arv@ command line tool.
-
-{% include 'tutorial_expectations' %}
-
-You will create a job to run the "hash" Crunch script.  The "hash" script computes the MD5 hash of each file in a collection.
-
-h2. Jobs
-
-Crunch pipelines consist of one or more jobs.  A "job" is a single run of a specific version of a Crunch script with a specific input.  You can also run jobs individually.
-
-A request to run a Crunch job are is described using a JSON object.  For example:
-
-
-
~$ cat >~/the_job <<EOF
-{
- "script": "hash",
- "repository": "arvados",
- "script_version": "master",
- "script_parameters": {
-  "input": "c1bad4b39ca5a924e481008009d94e32+210"
- },
- "no_reuse": "true"
-}
-EOF
-

-
-
-* @cat@ is a standard Unix utility that writes a sequence of input to standard output.
-* @<~/the_job@ redirects standard output to a file called @~/the_job@.
-* @"repository"@ is the name of a Git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench under "*Code repositories*":{{site.arvados_workbench_host}}/repositories.
-* @"script_version"@ specifies the version of the script that you wish to run.  This can be in the form of an explicit Git revision hash, a tag, or a branch.  Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
-* @"script"@ specifies the name of the script to run.  The script must be given relative to the @crunch_scripts/@ subdirectory of the Git repository.
-* @"script_parameters"@ are provided to the script.  In this case, the input is the PGP data Collection that we "put in Keep earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
-* Setting the @"no_reuse"@ flag tells Crunch not to reuse work from past jobs.  This helps ensure that you can watch a new Job process for the rest of this tutorial, without reusing output from a past run that you made, or somebody else marked as public.  (If you want to experiment, after the first run below finishes, feel free to edit this job to remove the @"no_reuse"@ line and resubmit it.  See what happens!)
-
-Use @arv job create@ to actually submit the job.  It should print out a JSON object which describes the newly created job:
-
-
-
~$ arv job create --job "$(cat ~/the_job)"
-{
- "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
- "kind":"arvados#job",
- "etag":"ax3cn7w9whq2hdh983yxvq09p",
- "uuid":"qr1hi-8i9sb-1pm1t02dezhupss",
- "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "created_at":"2013-12-16T20:44:32Z",
- "modified_by_client_uuid":"qr1hi-ozdt8-obw7foaks3qjyej",
- "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "modified_at":"2013-12-16T20:44:32Z",
- "updated_at":"2013-12-16T20:44:33Z",
- "submit_id":null,
- "priority":null,
- "script":"hash",
- "script_parameters":{
-  "input":"c1bad4b39ca5a924e481008009d94e32+210"
- },
- "script_version":"d9cd657b733d578ac0d2167dd75967aa4f22e0ac",
- "cancelled_at":null,
- "cancelled_by_client_uuid":null,
- "cancelled_by_user_uuid":null,
- "started_at":null,
- "finished_at":null,
- "output":null,
- "success":null,
- "running":null,
- "is_locked_by_uuid":null,
- "log":null,
- "runtime_constraints":{},
- "tasks_summary":{}
-}
-

-
-
-The job is now queued and will start running as soon as it reaches the front of the queue.  Fields to pay attention to include:
-
- * @"uuid"@ is the unique identifier for this specific job.
- * @"script_version"@ is the actual revision of the script used.  This is useful if the version was described using the "repository:branch" format.
-
-h2. Monitor job progress
-
-Go to "*Recent jobs*":{{site.arvados_workbench_host}}/jobs in Workbench.  Your job should be near the top of the table.  This table refreshes automatically.  When the job has completed successfully, it will show finished in the *Status* column.
-
-h2. Inspect the job output
-
-On the "Workbench Dashboard":{{site.arvados_workbench_host}}, look for the *Output* column of the *Recent jobs* table.  Click on the link under *Output* for your job to go to the files page with the job output.  The files page lists all the files that were output by the job.  Click on the link under the *file* column to view a file, or click on the download button  to download the output file.
-
-On the command line, you can use @arv job get@ to access a JSON object describing the output:
-
-
-
~$ arv job get --uuid qr1hi-8i9sb-xxxxxxxxxxxxxxx
-{
- "href":"https://qr1hi.arvadosapi.com/arvados/v1/jobs/qr1hi-8i9sb-1pm1t02dezhupss",
- "kind":"arvados#job",
- "etag":"1bk98tdj0qipjy0rvrj03ta5r",
- "uuid":"qr1hi-8i9sb-1pm1t02dezhupss",
- "owner_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "created_at":"2013-12-16T20:44:32Z",
- "modified_by_client_uuid":null,
- "modified_by_user_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "modified_at":"2013-12-16T20:44:55Z",
- "updated_at":"2013-12-16T20:44:55Z",
- "submit_id":null,
- "priority":null,
- "script":"hash",
- "script_parameters":{
-  "input":"c1bad4b39ca5a924e481008009d94e32+210"
- },
- "script_version":"d9cd657b733d578ac0d2167dd75967aa4f22e0ac",
- "cancelled_at":null,
- "cancelled_by_client_uuid":null,
- "cancelled_by_user_uuid":null,
- "started_at":"2013-12-16T20:44:36Z",
- "finished_at":"2013-12-16T20:44:53Z",
- "output":"dd755dbc8d49a67f4fe7dc843e4f10a6+54",
- "success":true,
- "running":false,
- "is_locked_by_uuid":"qr1hi-tpzed-9zdpkpni2yddge6",
- "log":"2afdc6c8b67372ffd22d8ce89d35411f+91",
- "runtime_constraints":{},
- "tasks_summary":{
-  "done":2,
-  "running":0,
-  "failed":0,
-  "todo":0
- }
-}
-

-
-
-* @"output"@ is the unique identifier for this specific job's output.  This is a Keep collection.  Because the output of Arvados jobs should be deterministic, the known expected output is dd755dbc8d49a67f4fe7dc843e4f10a6+54.
-
-Now you can list the files in the collection:
-
-
-
~$ arv keep ls dd755dbc8d49a67f4fe7dc843e4f10a6+54
-./md5sum.txt
-

-
-
-This collection consists of the @md5sum.txt@ file.  Use @arv-get@ to show the contents of the @md5sum.txt@ file:
-
-
-
~$ arv-get dd755dbc8d49a67f4fe7dc843e4f10a6+54/md5sum.txt
-44b8ae3fde7a8a88d2f7ebd237625b4f ./var-GS000016015-ASM.tsv.bz2
-

-
-
-This MD5 hash matches the MD5 hash which we "computed earlier":{{site.baseurl}}/user/tutorials/tutorial-keep.html.
-
-h2. The job log
-
-When the job completes, you can access the job log.  On the Workbench, visit "*Recent jobs*":{{site.arvados_workbench_host}}/jobs %(rarr)→% your job's UUID under the *uuid* column %(rarr)→% the collection link on the *log* row.
-
-On the command line, the Keep identifier listed in the @"log"@ field from @arv job get@ specifies a collection.  You can list the files in the collection:
-
-
-
~$ arv keep ls xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91
-./qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt
-

-
-
-The log collection consists of one log file named with the job's UUID.  You can access it using @arv-get@:
-
-
-
~$ arv-get xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx+91/qr1hi-8i9sb-xxxxxxxxxxxxxxx.log.txt
-2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  check slurm allocation
-2013-12-16_20:44:35 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  node compute13 - 8 slots
-2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  start
-2013-12-16_20:44:36 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  Install revision d9cd657b733d578ac0d2167dd75967aa4f22e0ac
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  Clean-work-dir exited 0
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  Install exited 0
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  script hash
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  script_version d9cd657b733d578ac0d2167dd75967aa4f22e0ac
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  script_parameters {"input":"c1bad4b39ca5a924e481008009d94e32+210"}
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  runtime_constraints {"max_tasks_per_node":0}
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  start level 0
-2013-12-16_20:44:37 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  status: 0 done, 0 running, 1 todo
-2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 job_task qr1hi-ot0gb-23c1k3kwrf8da62
-2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 child 7681 started on compute13.1
-2013-12-16_20:44:38 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  status: 0 done, 1 running, 0 todo
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 child 7681 on compute13.1 exit 0 signal 0 success=true
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 success in 1 seconds
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 0 output
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  wait for last 0 children to finish
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  status: 1 done, 0 running, 1 todo
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  start level 1
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  status: 1 done, 0 running, 1 todo
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 job_task qr1hi-ot0gb-iwr0o3unqothg28
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 child 7716 started on compute13.1
-2013-12-16_20:44:39 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  status: 1 done, 1 running, 0 todo
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 child 7716 on compute13.1 exit 0 signal 0 success=true
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 success in 13 seconds
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575 1 output dd755dbc8d49a67f4fe7dc843e4f10a6+54
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  wait for last 0 children to finish
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  status: 2 done, 0 running, 0 todo
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  release job allocation
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  Freeze not implemented
-2013-12-16_20:44:52 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  collate
-2013-12-16_20:44:53 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  output dd755dbc8d49a67f4fe7dc843e4f10a6+54+K@qr1hi
-2013-12-16_20:44:53 qr1hi-8i9sb-xxxxxxxxxxxxxxx 7575  finish
-

-
diff --git a/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid b/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
index 2375e8b3d5..180e087824 100644
--- a/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-collection-lifecycle.html.textile.liquid
@@ -39,7 +39,7 @@ A collection can be deleted using either the arv command line tool or the workbe
 h3. Trashing a collection using arv command line tool
 
 
-arv collection delete --uuid=qr1hi-4zz18-xxxxxxxxxxxxxxx
+arv collection delete --uuid=zzzzz-4zz18-xxxxxxxxxxxxxxx
 

 
 h3. Trashing a collection using workbench
@@ -61,7 +61,7 @@ arv collection list --include-trash=true --filters '[["is_trashed", "=", "true"]
 You can then untrash a particular collection using arv using it's uuid.
 
 
-arv collection untrash --uuid=qr1hi-4zz18-xxxxxxxxxxxxxxx
+arv collection untrash --uuid=zzzzz-4zz18-xxxxxxxxxxxxxxx
 

 
 h3. Un-trashing a collection using workbench
diff --git a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
index f206d302de..c73675bf11 100644
--- a/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep-get.html.textile.liquid
@@ -65,10 +65,10 @@ If your cluster is "configured to be part of a federation":{{site.baseurl}}/admi
 
 If you request a collection by portable data hash, it will first search the home cluster, then search federated clusters.
 
-You may also request a collection by UUID.  In this case, it will contact the cluster named in the UUID prefix (in this example, @qr1hi@).
+You may also request a collection by UUID.  In this case, it will contact the cluster named in the UUID prefix (in this example, @zzzzz@).
 
 
-
~$ arv-get qr1hi-4zz18-fw6dnjxtkvzdewt/ .
+
~$ arv-get zzzzz-4zz18-fw6dnjxtkvzdewt/ .
 

 
 
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index ec7086db96..5dd87c2633 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -25,12 +25,12 @@ To upload a file to Keep using @arv-put@:
 
~$ arv-put var-GS000016015-ASM.tsv.bz2
 216M / 216M 100.0%
 Collection saved as ...
-qr1hi-4zz18-xxxxxxxxxxxxxxx
+zzzzz-4zz18-xxxxxxxxxxxxxxx
 

 
 
 
-The output value @qr1hi-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
+The output value @zzzzz-4zz18-xxxxxxxxxxxxxxx@ is the uuid of the Arvados collection created.
 
 Note: The file used in this example is a freely available TSV file containing variant annotations from the "Personal Genome Project (PGP)":http://www.pgp-hms.org participant "hu599905":https://my.pgp-hms.org/profile/hu599905), downloadable "here":https://warehouse.pgp-hms.org/warehouse/f815ec01d5d2f11cb12874ab2ed50daa+234+K@ant/var-GS000016015-ASM.tsv.bz2. Alternatively, you can replace @var-GS000016015-ASM.tsv.bz2@ with the name of any file you have locally, or you could get the TSV file by "downloading it from Keep.":{{site.baseurl}}/user/tutorials/tutorial-keep-get.html
 
@@ -44,7 +44,7 @@ Note: The file used in this example is a freely available TSV file containing va
 ~$ arv-put tmp
 0M / 0M 100.0%
 Collection saved as ...
-qr1hi-4zz18-yyyyyyyyyyyyyyy
+zzzzz-4zz18-yyyyyyyyyyyyyyy
 

 
 
diff --git a/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid b/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
index dd537c46ac..4e10eff018 100644
--- a/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
+++ b/doc/user/tutorials/writing-cwl-workflow.html.textile.liquid
@@ -35,9 +35,9 @@ Use @--create-workflow@ to register a CWL workflow with Arvados.  This enables y
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --create-workflow bwa-mem.cwl
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Upload local files: "bwa-mem.cwl"
-2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to qr1hi-4zz18-7e0hedrmkuyoei3
-2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template qr1hi-p5p6p-rjleou1dwr167v5
-qr1hi-p5p6p-rjleou1dwr167v5
+2016-07-01 12:21:01 arvados.arv-run[15796] INFO: Uploaded to zzzzz-4zz18-7e0hedrmkuyoei3
+2016-07-01 12:21:01 arvados.cwl-runner[15796] INFO: Created template zzzzz-p5p6p-rjleou1dwr167v5
+zzzzz-p5p6p-rjleou1dwr167v5
 

 
 
@@ -47,9 +47,9 @@ You can provide a partial input file to set default values for the workflow inpu
 
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner --name "My workflow with defaults" --create-workflow bwa-mem.cwl bwa-mem-template.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Upload local files: "bwa-mem.cwl"
-2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Uploaded to qr1hi-4zz18-0f91qkovk4ml18o
-2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template qr1hi-p5p6p-0deqe6nuuyqns2i
-qr1hi-p5p6p-zuniv58hn8d0qd8
+2016-07-01 14:09:50 arvados.arv-run[3730] INFO: Uploaded to zzzzz-4zz18-0f91qkovk4ml18o
+2016-07-01 14:09:50 arvados.cwl-runner[3730] INFO: Created template zzzzz-p5p6p-0deqe6nuuyqns2i
+zzzzz-p5p6p-zuniv58hn8d0qd8
 

 
 
@@ -58,10 +58,10 @@ h3. Running registered workflows at the command line
 You can run a registered workflow at the command line by its UUID:
 
 
-
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner qr1hi-p5p6p-zuniv58hn8d0qd8 --help
+
~/arvados/doc/user/cwl/bwa-mem$ arvados-cwl-runner zzzzz-p5p6p-zuniv58hn8d0qd8 --help
 /home/peter/work/scripts/venv/bin/arvados-cwl-runner 0d62edcb9d25bf4dcdb20d8872ea7b438e12fc59 1.0.20161209192028, arvados-python-client 0.1.20161212125425, cwltool 1.0.20161207161158
-Resolved 'qr1hi-p5p6p-zuniv58hn8d0qd8' to 'keep:655c6cd07550151b210961ed1d3852cf+57/bwa-mem.cwl'
-usage: qr1hi-p5p6p-zuniv58hn8d0qd8 [-h] [--PL PL] --group_id GROUP_ID
+Resolved 'zzzzz-p5p6p-zuniv58hn8d0qd8' to 'keep:655c6cd07550151b210961ed1d3852cf+57/bwa-mem.cwl'
+usage: zzzzz-p5p6p-zuniv58hn8d0qd8 [-h] [--PL PL] --group_id GROUP_ID
                                    --read_p1 READ_P1 [--read_p2 READ_P2]
                                    [--reference REFERENCE] --sample_id
                                    SAMPLE_ID
@@ -164,10 +164,10 @@ You can make a workflow file directly executable (@cwl-runner@ should be an alia
 
~/arvados/doc/user/cwl/bwa-mem$ ./bwa-mem.cwl bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {
@@ -192,10 +192,10 @@ cwl:tool: bwa-mem.cwl
 
~/arvados/doc/user/cwl/bwa-mem$ ./bwa-mem-input.yml
 arvados-cwl-runner 1.0.20160628195002, arvados-python-client 0.1.20160616015107, cwltool 1.0.20160629140624
 2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Upload local files: "bwa-mem.cwl"
-2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to qr1hi-4zz18-h7ljh5u76760ww2
-2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job qr1hi-8i9sb-fm2n3b1w0l6bskg
-2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Running
-2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (qr1hi-8i9sb-fm2n3b1w0l6bskg) is Complete
+2016-06-30 14:56:36 arvados.arv-run[27002] INFO: Uploaded to zzzzz-4zz18-h7ljh5u76760ww2
+2016-06-30 14:56:40 arvados.cwl-runner[27002] INFO: Submitted job zzzzz-8i9sb-fm2n3b1w0l6bskg
+2016-06-30 14:56:41 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Running
+2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Job bwa-mem.cwl (zzzzz-8i9sb-fm2n3b1w0l6bskg) is Complete
 2016-06-30 14:57:12 arvados.cwl-runner[27002] INFO: Overall process status is success
 {
     "aligned_sam": {