navsection: userguide
title: "Using arv-copy"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
This tutorial describes how to copy Arvados objects from one cluster to another by using @arv-copy@.
h2. arv-copy
-@arv-copy@ allows users to copy collections, pipeline templates, and pipeline instances from one cluster to another. By default, @arv-copy@ will recursively go through a template or instance and copy all dependencies associated with the object.
+@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 our <a href="https://cloud.curoverse.com/">beta cloud instance *qr1hi*</a> 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 <a href="https://playground.arvados.org/">Arvados playground</a>, 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 for the clusters to be able to communicate with each other, you must create custom configuration files for both clusters. First, go to your *Manage account* page in Workbench and 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 *uuid_prefix*.conf. In our example, let's make two files, one for *qr1hi* and one for *dst_cluster*. From your *Manage account* 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 <span class="fa fa-lg fa-user"></span> <span class="caret"></span> 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 in @~/.config/arvados@, one for each cluster. The names of the files must have the format of *ClusterID.conf*. Navigate to the *Current token* page on each of *pirca* and *dstcl* to get 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.
+The config file consists of two lines, one for ARVADOS_API_HOST and one for ARVADOS_API_TOKEN:
-<notextile>
-<pre><code>~$ <span class="userinput">cd ~/.config/arvados</span>
-~$ <span class="userinput">echo "ARVADOS_API_HOST=qr1hi.arvadosapi.com" >> qr1hi.conf</span>
-~$ <span class="userinput">echo "ARVADOS_API_TOKEN=123456789abcdefghijkl" >> qr1hi.conf</span>
-~$ <span class="userinput">echo "ARVADOS_API_HOST=dst_cluster.arvadosapi.com" >> dst_cluster.conf</span>
-~$ <span class="userinput">echo "ARVADOS_API_TOKEN=987654321lkjihgfedcba" >> dst_cluster.conf</span>
-</code></pre>
-</notextile>
+<pre>
+ARVADOS_API_HOST=zzzzz.arvadosapi.com
+ARVADOS_API_TOKEN=v2/zzzzz-gj3su-xxxxxxxxxxxxxxx/123456789abcdefghijkl
+</pre>
-Now you're ready to copy between *qr1hi* and *dst_cluster*!
+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. In our example, you need two files, @~/.config/arvados/pirca.conf@ and @~/.config/arvados/dstcl.conf@.
+
+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 displace page in the collection summary area (top left box), or from the URL bar (the part after @collections/...@)
+First, determine the uuid or portable data hash 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 <a href="https://cloud.curoverse.com/collections/qr1hi-4zz18-tci4vn4fa95w0zx">lobSTR v.3 project on cloud.curoverse.com</a>.
+Now copy the collection from *pirca* to *dstcl*. We will use the uuid @jutro-4zz18-tv416l321i4r01e@ as an example. You can find this collection on <a href="https://playground.arvados.org/collections/jutro-4zz18-tv416l321i4r01e">playground.arvados.org</a>.
<notextile>
-<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster qr1hi-4zz18-tci4vn4fa95w0zx</span>
-qr1hi-4zz18-tci4vn4fa95w0zx: 6.1M / 6.1M 100.0%
-arvados.arv-copy[1234] INFO: Success: created copy with uuid dst_cluster-4zz18-8765943210cdbae
+<pre><code>~$ <span class="userinput">arv-copy --src pirca --dst dstcl jutro-4zz18-tv416l321i4r01e</span>
+jutro-4zz18-tv416l321i4r01e: 6.1M / 6.1M 100.0%
+arvados.arv-copy[1234] INFO: Success: created copy with uuid dstcl-4zz18-xxxxxxxxxxxxxxx
</code></pre>
</notextile>
-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 inside of 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.
+You can also copy by content address:
-<notextile> <pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --project-uuid dst_cluster-j7d0g-a894213ukjhal12 qr1hi-4zz18-tci4vn4fa95w0zx</span>
+<notextile>
+<pre><code>~$ <span class="userinput">arv-copy --src pirca --dst dstcl 2463fa9efeb75e099685528b3b9071e0+438</span>
+2463fa9efeb75e099685528b3b9071e0+438: 6.1M / 6.1M 100.0%
+arvados.arv-copy[1234] INFO: Success: created copy with uuid dstcl-4zz18-xxxxxxxxxxxxxxx
</code></pre>
</notextile>
-h3. How to copy a pipeline template or pipeline instance
+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 an existing project, you can specify the project you want it to be in using the tag @--project-uuid@ followed by the project uuid.
-{% include 'arv_copy_expectations' %}
+For example, this will copy the collection to project @dstcl-j7d0g-a894213ukjhal12@ in the destination cluster.
-We will use the uuid @qr1hi-d1hrv-nao0ohw8y7dpf84@ as an example pipeline instance.
-
-<notextile>
-<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial qr1hi-d1hrv-nao0ohw8y7dpf84</span>
-To git@git.dst_cluster.arvadosapi.com:$USER/tutorial.git
- * [new branch] git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d -> git_git_qr1hi_arvadosapi_com_arvados_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d
-arvados.arv-copy[19694] INFO: Success: created copy with uuid dst_cluster-d1hrv-rym2h5ub9m8ofwj
+<notextile> <pre><code>~$ <span class="userinput">arv-copy --src pirca --dst dstcl --project-uuid dstcl-j7d0g-a894213ukjhal12 jutro-4zz18-tv416l321i4r01e
</code></pre>
</notextile>
-New branches in the destination git repo will be created for each branch used in the pipeline template. For example, if your source branch was named ac21f0d45a76294aaca0c0c0fdf06eb72d03368d, your new branch will be named @git_git_qr1hi_arvadosapi_com_reponame_git_ac21f0d45a76294aaca0c0c0fdf06eb72d03368d@.
-
-By default, if you copy a pipeline instance recursively, you will find that the template as well as all the dependencies are in your home project.
+Additionally, if you need to specify the storage classes where to save the copied data on the destination cluster, you can do that by using the @--storage-classes LIST@ argument, where @LIST@ is a comma-separated list of storage class names.
-If you would like to copy the object without dependencies, you can use the @--no-recursive@ tag.
+h3. How to copy a workflow
-For example, we can copy the same object using this tag.
+We will use the uuid @jutro-7fd4e-mkmmq53m1ze6apx@ as an example workflow.
<notextile>
-<pre><code>~$ <span class="userinput">arv-copy --src qr1hi --dst dst_cluster --dst-git-repo $USER/tutorial --no-recursive qr1hi-d1hrv-nao0ohw8y7dpf84</span>
+<pre><code>~$ <span class="userinput">arv-copy --src jutro --dst pirca --project-uuid pirca-j7d0g-ecak8knpefz8ere jutro-7fd4e-mkmmq53m1ze6apx</span>
+ae480c5099b81e17267b7445e35b4bc7+180: 23M / 23M 100.0%
+2463fa9efeb75e099685528b3b9071e0+438: 156M / 156M 100.0%
+jutro-4zz18-vvvqlops0a0kpdl: 94M / 94M 100.0%
+2020-08-19 17:04:13 arvados.arv-copy[4789] INFO:
+2020-08-19 17:04:13 arvados.arv-copy[4789] INFO: Success: created copy with uuid pirca-7fd4e-s0tw9rfbkpo2fmx
</code></pre>
</notextile>
+
+The name, description, and workflow definition from the original workflow will be used for the destination copy. In addition, any *collections* and *docker images* referenced in the source workflow definition will also be copied to the destination.
+
+If you would like to copy the object without dependencies, you can use the @--no-recursive@ flag.
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