From: Peter Amstutz Date: Sat, 26 Jul 2014 03:42:40 +0000 (-0400) Subject: 3232: Reorganized user guide X-Git-Tag: 1.1.0~2376^2~7 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/77f1129ec53edffb5ed5a859106675cf262977e8?hp=fa3f6860158dda089c0b4b96c346bbc643232421 3232: Reorganized user guide Major changes: * Now separate sections for how to use Arvados and how to develop for Arvados * Running a pipeline in workbench tutorial is simpler, involves fewer steps * New example pipelines which are biologically relevant * Working with data is its own section, and directs user to instructions on installing Python SDK in order to upload data remotely * Includes docker_image runtime constraint in examples * Introduces "run-command" wrapper before writing a script with the Python SDK * Added font awesome CSS and glyphs so documentation can use the same icons as Workbench. --- diff --git a/doc/_config.yml b/doc/_config.yml index a6fb3d65ae..f84590712d 100644 --- a/doc/_config.yml +++ b/doc/_config.yml @@ -4,7 +4,7 @@ # workbench, use /doc here and add a symlink at # apps/workbench/public/doc pointing to ../../../doc/.site # You can also set these on the command line: -# $ rake generate baseurl=/example arvados_api_host=example.comA +# $ rake generate baseurl=/example arvados_api_host=example.com baseurl: arvados_api_host: localhost @@ -16,31 +16,32 @@ navbar: userguide: - Getting Started: - user/index.html.textile.liquid + - user/getting_started/community.html.textile.liquid + - Run a pipeline using Workbench: - user/getting_started/workbench.html.textile.liquid + - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid + - Access an Arvados virtual machine: - user/getting_started/ssh-access-unix.html.textile.liquid - user/getting_started/ssh-access-windows.html.textile.liquid - user/getting_started/check-environment.html.textile.liquid - - user/getting_started/community.html.textile.liquid - - Tutorials: + - user/reference/api-tokens.html.textile.liquid + - Working with data sets: - user/tutorials/tutorial-keep.html.textile.liquid + - user/tutorials/tutorial-keep-get.html.textile.liquid + - user/tutorials/tutorial-keep-mount.html.textile.liquid + - user/topics/keep.html.textile.liquid + - Run a pipeline on the command line: + - user/topics/running-pipeline-command-line.html.textile.liquid + - user/reference/sdk-cli.html.textile.liquid + - Develop a new pipeline: - user/tutorials/intro-crunch.html.textile.liquid - - user/tutorials/tutorial-pipeline-workbench.html.textile.liquid - - user/tutorials/tutorial-firstscript.html.textile.liquid - - user/tutorials/tutorial-new-pipeline.html.textile.liquid - user/tutorials/running-external-program.html.textile.liquid - - Intermediate topics: - - user/topics/running-pipeline-command-line.html.textile.liquid - - user/topics/tutorial-job1.html.textile.liquid + - user/tutorials/tutorial-firstscript.html.textile.liquid - user/topics/tutorial-job-debug.html.textile.liquid - user/topics/tutorial-parallel.html.textile.liquid - - user/topics/tutorial-trait-search.html.textile.liquid - - user/topics/tutorial-gatk-variantfiltration.html.textile.liquid - - user/topics/keep.html.textile.liquid - - Examples: - user/examples/crunch-examples.html.textile.liquid - - Reference: - - user/reference/api-tokens.html.textile.liquid - - user/reference/sdk-cli.html.textile.liquid + - Query the metadata database: + - user/topics/tutorial-trait-search.html.textile.liquid - Arvados License: - user/copying/copying.html.textile.liquid - user/copying/agpl-3.0.html diff --git a/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid b/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid new file mode 100644 index 0000000000..dcce375439 --- /dev/null +++ b/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid @@ -0,0 +1,65 @@ +{ + "name": "Tutorial align using bwa mem and SortSam", + "components": { + "bwa-mem": { + "script": "run-command", + "script_version": "master", + "repository": "arvados", + "script_parameters": { + "command": [ + "bwa", + "mem", + "-t", + "$(node.cores)", + "-R", + "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id", + "$(glob $(dir $(reference_collection))/*.fasta)", + "$(glob $(dir $(sample))/*_1.fastq)", + "$(glob $(dir $(sample))/*_2.fastq)" + ], + "reference_collection": { + "required": true, + "dataclass": "Collection" + }, + "sample": { + "required": true, + "dataclass": "Collection" + }, + "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam" + }, + "runtime_constraints": { + "docker_image": "arvados/jobs-java-bwa-samtools" + } + } + }, + "SortSam": { + "script": "run-command", + "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2", + "repository": "arvados", + "script_parameters": { + "command": [ + "java", + "-Xmx4g", + "-Djava.io.tmpdir=$(tmpdir)", + "-jar", + "$(dir $(picard))/SortSam.jar", + "CREATE_INDEX=True", + "SORT_ORDER=coordinate", + "VALIDATION_STRINGENCY=LENIENT", + "INPUT=$(glob $(dir $(input))/*.sam)", + "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam" + ], + "input": { + "output_of": "bwa-mem" + }, + "picard": { + "required": true, + "dataclass": "Collection", + "default": "88447c464574ad7f79e551070043f9a9+1970" + } + }, + "runtime_constraints": { + "docker_image": "arvados/jobs-java-bwa-samtools" + } + } +} \ No newline at end of file diff --git a/doc/_includes/_tutorial_expectations.liquid b/doc/_includes/_tutorial_expectations.liquid index 86ac64c90d..523d3a7bb7 100644 --- a/doc/_includes/_tutorial_expectations.liquid +++ b/doc/_includes/_tutorial_expectations.liquid @@ -1 +1 @@ -*This tutorial assumes that you are logged into an Arvados VM instance ("Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login), and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html* +*This tutorial assumes that you are logged into an Arvados VM instance (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login), and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html* diff --git a/doc/_layouts/default.html.liquid b/doc/_layouts/default.html.liquid index 4585b7032a..88da01b178 100644 --- a/doc/_layouts/default.html.liquid +++ b/doc/_layouts/default.html.liquid @@ -12,6 +12,7 @@ + - +