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‎_sources/check-recipe.rst.txt‎

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@@ -48,6 +48,7 @@ Example
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#!/bin/sh
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set -eo pipefail -o nounset
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wget --quiet --no-check-certificate \
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-O hg19-phastcons-ucsc-v1.bw \
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http://hgdownload.cse.ucsc.edu/goldenpath/hg19/phastCons100way/hg19.100way.phastCons.bw
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* Using :code:`ggd make-recipe` to create a ggd recipe::
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--author mjc --ggd_version 1 \
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--data_version 09-Feb-2014 \
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--summary 'phastCons scores for MSA of 99 genomes to hg19' \
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-e hg19.100way.phastCons.bw -k phastCons \
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-k conservation get_data.sh
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-e hg19-phastcons-ucsc-v1.bw -k phastCons \
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-k conservation phastcons-ucsc get_data.sh
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* A new directory called **hg19-phastcons** is now present in the current working directory
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* The **hg19-phastcons** directory contains three files: **meta.yaml**, **post-link.sh**, and **recipe.sh**
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* Lets say the path to **hg19-phastcons** is ``/user/home/hg19-phastcons/``
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* A new directory called **hg19-phastcons-ucsc-v1** is now present in the current working directory
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* The **hg19-phastcons-ucsc-v1** directory contains three files: **meta.yaml**, **post-link.sh**, and **recipe.sh**
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* Lets say the path to **hg19-phastcons-ucsc-v1** is ``/user/home/hg19-phastcons-ucsc-v1/``
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* Using :code:`ggd check-recipe` we will build, install, and test the new **hg19-phastcons** recipe::
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* Using :code:`ggd check-recipe` we will build, install, and test the new **hg19-phastcons-ucsc-v1** recipe::
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$ ggd check-recipe /user/home/hg19-phastcons/
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$ ggd check-recipe /user/home/hg19-phastcons-ucsc-v1/
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No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11
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WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.11
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INFO:conda_build.variants:Adding in variants from internal_defaults
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INFO:conda_build.metadata:Attempting to finalize metadata for hg19-phastcons
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INFO:conda_build.build:Packaging hg19-phastcons
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INFO:conda_build.build:Packaging hg19-phastcons-1-0
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No files or script found for output hg19-phastcons
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WARNING:conda_build.build:No files or script found for output hg19-phastcons
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/TMP/hg19-phastcons-1-0.tar.bz2: C1115 Found invalid license "None" in info/index.json
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/TMP/hg19-phastcons-1-0.tar.bz2: C1134 Found pre/post link file "bin/.hg19-phastcons-post-link.sh" in archive
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INFO:conda_build.metadata:Attempting to finalize metadata for hg19-phastcons-ucsc-v1
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INFO:conda_build.build:Packaging hg19-phastcons-ucsc-v1
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INFO:conda_build.build:Packaging hg19-phastcons-ucsc-v1-1-0
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No files or script found for output hg19-phastcons-ucsc-v1
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WARNING:conda_build.build:No files or script found for output hg19-phastcons-ucsc-v1
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/TMP/hg19-phastcons-ucsc-v1-1-0.tar.bz2: C1115 Found invalid license "None" in info/index.json
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/TMP/hg19-phastcons-ucsc-v1-1-0.tar.bz2: C1134 Found pre/post link file "bin/.hg19-phastcons-ucsc-v1-post-link.sh" in archive
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INFO:conda_build.variants:Adding in variants from /TMP/info/recipe/conda_build_config.yaml
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Solving environment: done
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## Package Plan ##
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environment location: /scratch/ucgd/lustre/work/u1138933/anaconda2
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environment location: <conda root>
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added / updated specs:
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- hg19-phastcons
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- hg19-phastcons-ucsc-v1
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The following packages will be downloaded:
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package | build
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---------------------------|-----------------
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hg19-phastcons-1 | 0 5 KB local
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hg19-phastcons-ucsc-v1-1 | 0 5 KB local
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The following NEW packages will be INSTALLED:
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hg19-phastcons: 1-0 local
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hg19-phastcons-ucsc-v1: 1-0 local
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Downloading and Extracting Packages
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hg19-phastcons-1 | 5 KB | ############################ | 100%
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hg19-phastcons-ucsc-v1-1 | 5 KB | ############################ | 100%
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Preparing transaction: done
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Verifying transaction: done
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Executing transaction: done
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modified files:
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:: /<conda root>/share/ggd/Homo_sapiens/hg19/hg19-phastcons/1/hg19.100way.phastCons.bw
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:: /<conda root>/share/ggd/Homo_sapiens/hg19/hg19-phastcons-ucsc-v1/1/hg19-phastcons-ucsc-v1.bw
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checking /scratch/ucgd/lustre/work/u1138933/anaconda2/share/ggd/Homo_sapiens/hg19/hg19-phastcons/1/hg19.100way.phastCons.bw
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checking <conda root>/share/ggd/Homo_sapiens/hg19/hg19-phastcons-ucsc-v1/1/hg19-phastcons-ucsc-v1.bw
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****************************
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* Successful recipe check! *

‎_sources/contribute-recipe.rst.txt‎

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@@ -58,9 +58,9 @@ The following will outline steps used to create the hg19-gaps ggd data recipe:
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| gzip -dc \
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| awk -v OFS="\t" 'BEGIN {print "#chrom\tstart\tend\tsize\ttype\tstrand"} {print $2,$3,$4,$7,$8,"+"}' \
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| gsort /dev/stdin $genome \
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| bgzip -c > gaps.bed.gz
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| bgzip -c > hg19-gaps-ucsc-v1.bed.gz
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tabix gaps.bed.gz
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tabix hg19-gaps-ucsc-v1.bed.gz
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* In this data processing script please change the resulting data file names to be short and include all necessary
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genomic file extentions. (See the NOTE bellow)
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$ ggd make-recipe -s Homo_sapiens -g hg19 --author mjc \
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--ggd_version 1 --data_version 27-Apr-2009 \
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--summary 'Assembly gaps from USCS' \
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-k gaps -k region gaps hg19_data_recipe.sh
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-k gaps -k region gaps-ucsc hg19_data_recipe.sh
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The :code:`ggd make-recipe` tool transforms the bash script you created into a data recipe. Running the above code will create
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a data recipe called *hg19-gaps*, which will be a directory and will contain three files. For more information on the
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a data recipe called *hg19-gaps-ucsc-v1*, which will be a directory and will contain three files. For more information on the
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:code:`ggd make-recipe` command see :ref:`make-recipe <ggd-make-recipe>`.
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4. Build, install, and check the data recipe
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Using the hg19-gaps recipe created in step 3, run the following command::
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$ ggd check-recipe hg19-gaps
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$ ggd check-recipe hg19-gaps-ucsc-v1
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Or if you are in a different directory on your machine run::
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$ ggd check-recipe <Path_To_hg19-gaps>
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$ ggd check-recipe <Path_To_hg19-gaps-ucsc-v1>
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This command will build, install, and check the validity of the new ggd data recipe.
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For more information about :code:`ggd check-recipe` see :ref:`check-recipe <ggd-check-recipe>`
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For the hg19-gaps recipe above you would use the following commands::
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$ mv hg19-gaps /<forked ggd-recipes>/recipes/genomics/Homo_sapiens/hg19/
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$ mv hg19-gaps-ucsc-v1 /<forked ggd-recipes>/recipes/genomics/Homo_sapiens/hg19/
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Once the recipe is there you will need to add the recipe to your forked ggd-recipe repo.
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Navigate to the forked ggd-recipe directory and use the following commands:
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* Add the recipe to the git repo::
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$ git add /recipes/genomics/Homo_sapiens/hg19/hg19-gaps/
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$ git add /recipes/genomics/Homo_sapiens/hg19/hg19-gaps-ucsc-v1/
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* Commit the addition to the repo (A text editor will open up. Add a comment about the new recipe and save it)::
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‎_sources/ggd-search.rst.txt‎

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$ ggd search -t reference
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grch37-reference-genome
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grch37-reference-genome-1000g-v1
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Summary: GRCh37 reference genome from 1000 genomes
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Species: Homo_sapiens
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Genome Build: GRCh37
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Keywords: ref, reference
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Data Version: phase2_reference
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To install run:
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ggd install grch37-reference-genome
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ggd install grch37-reference-genome-1000g-v1
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grch38-reference-genome
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grch38-reference-genome-ensembl-v1
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2. Simple example with two search terms:
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$ ggd search -t repeat masker
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hg38-repeatmasker
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hg38-repeatmasker-ucsc-v1
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Summary: RepeatMasker track from UCSC
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Species: Homo_sapiens
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Genome Build: hg38
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Keywords: rmsk, region
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Data Version: 06-Mar-2014
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To install run:
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ggd install hg38-repeatmasker
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ggd install hg38-repeatmasker-ucsc-v1
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hg19-repeatmasker
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hg19-repeatmasker-ucsc-v1
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Summary: RepeatMasker track from UCSC
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Species: Homo_sapiens
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Genome Build: hg19
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Keywords: rmsk, region
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Data Version: 27-Apr-2009
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ggd install hg19-repeatmasker
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ggd install hg19-repeatmasker-ucsc-v1
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3. Example using ``-g``, ``-s``, and ``-k`` flags to filter the results:
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$ ggd search -t reference genome -g grch37 -s Homo_sapiens -k ref
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grch37-reference-genome
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grch37-reference-genome-1000g-v1
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Summary: GRCh37 reference genome from 1000 genomes
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Species: Homo_sapiens
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Genome Build: GRCh37
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Keywords: ref, reference
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Data Version: phase2_reference
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ggd install grch37-reference-genome
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ggd install grch37-reference-genome-1000g-v1

‎_sources/index.rst.txt‎

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$ ggd search -t reference genome
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grch37-reference-genome
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Summary: GRCh37 reference genome from 1000 genomes
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Species: Homo_sapiens
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Genome Build: GRCh37
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Keywords: ref, reference
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Data Version: phase2_reference
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ggd install grch37-reference-genome
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grch38-reference-genome-ensembl
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Summary: GRCh37 reference genome from Ensembl
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Species: Homo_sapiens
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Genome Build: GRCh38
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Keywords: ref, reference
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Data Version: Release-95
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ggd install grch38-reference-genome-ensembl
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grch37-reference-genome-1000g-v1
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Summary: GRCh37 reference genome from 1000 genomes
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Species: Homo_sapiens
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Genome Build: GRCh37
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Keywords: ref, reference, fasta-file
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Data Version: phase2_reference
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ggd install grch37-reference-genome-1000g-v1
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grch37-reference-genome-ensembl-v1
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Summary: The GRCh37 reference genome from Ensembl. Release 75. Primary Assembly file
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Species: Homo_sapiens
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Genome Build: GRCh37
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Keywords: ref, reference, Ensembl, Release75
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Data Version: Release-75
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To install run:
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ggd install grch37-reference-genome-ensembl-v1
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grch38-reference-genome-ensembl-v1
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Summary: The GRCh38 reference genome from Ensembl. Release 95. Primary Assembly file
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Species: Homo_sapiens
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Genome Build: GRCh38
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Keywords: ref, reference, genome, Ensembl
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Data Version: Release-95
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To install run:
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ggd install grch38-reference-genome-ensembl-v1
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. . .
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# (See ggd install)
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#******************************
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$ ggd install grch38-reference-genome-ensembl
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$ ggd install grch38-reference-genome-ensembl-v1
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Looking for grch38-reference-genome-ensembl in the 'ggd-genomics' channel
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Looking for grch38-reference-genome-ensembl-v1 in the 'ggd-genomics' channel
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grch38-reference-genome-ensembl exists in ggd-genomics
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grch38-reference-genome-ensembl-v1 exists in ggd-genomics
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grch38-reference-genome-ensembl is not installed on your system
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grch38-reference-genome-ensembl-v1 is not installed on your system
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grch38-reference-genome-ensembl has not been installed by conda
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grch38-reference-genome-ensembl-v1 has not been installed by conda
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Installing grch38-reference-genome-ensembl
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Installing grch38-reference-genome-ensembl-v1
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Solving environment:
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## Package Plan ##
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environment location: <conda root>
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- grch38-reference-genome-ensembl
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- grch38-reference-genome-ensembl-v1
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The following packages will be downloaded:
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grch38-reference-genome-ensembl | 0 6 KB ggd-genomics
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grch38-reference-genome-ensembl-v1 | 0 6 KB ggd-genomics
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The following NEW packages will be INSTALLED:
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grch38-reference-genome-ensembl: 1-0 ggd-genomics
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Downloading and Extracting Packages
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grch38-reference-genome-ensembl | 6 KB | ###########################################################################################
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grch38-reference-genome-ensembl-v1 | 6 KB | ###########################################################################################
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Preparing transaction: done
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Verifying transaction: done
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Executing transaction: done
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***************************
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Active environment variables:
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> $ggd_grch38_reference_genome-ensembl
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> $ggd_grch38_reference_genome-ensembl_v1_dir
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> $ggd_grch38_reference_genome-ensembl_v1_file
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***************************
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$ ggd list-files grch38-reference-genome-ensembl
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$ ggd list-files grch38-reference-genome-ensembl-v1
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<conda root>/ share/ggd/Homo_sapiens/GRCh38/grch38-reference-genome-ensembl/1/grch38.fa
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<conda root>/share/ggd/Homo_sapiens/GRCh38/grch38-reference-genome-ensembl/1/grch38.fa.fai
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<conda root>/ share/ggd/Homo_sapiens/GRCh38/grch38-reference-genome-ensembl-ensembl-v1/1/grch38.fa
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<conda root>/share/ggd/Homo_sapiens/GRCh38/grch38-reference-genome-ensembl-ensembl-v1/1/grch38.fa.fai
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#******************************
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#4. Use files
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# To use the downloaded data packages you can use the full file path from running `ggd list-files`
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# or the environment variables created during installation
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# For more info see the `Using installed data` tab.
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#******************************
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‎_sources/install.rst.txt‎

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.. code-block:: bash
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$ ggd install hg19-gaps
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$ ggd install hg19-gaps-ucsc-v1
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Looking for hg19-gaps in the 'ggd-genomics' channel
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Looking for hg19-gaps-ucsc-v1 in the 'ggd-genomics' channel
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hg19-gaps exists in ggd-genomics
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hg19-gaps-ucsc-v1 exists in ggd-genomics
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hg19-gaps is not installed on your system
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hg19-gaps-ucsc-b1 is not installed on your system
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hg19-gaps has not been installed by conda
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hg19-gaps-ucsc-v1 has not been installed by conda
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Installing hg19-gaps
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Installing hg19-gaps-uscs-v1
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Solving environment:
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## Package Plan ##
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environment location: <conda root>
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added / updated specs:
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- hg19-gaps
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- hg19-gaps-ucsc-b1
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The following packages will be downloaded:
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package | build
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hg19-gaps-1 | 0 6 KB ggd-genomics
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hg19-gaps-uscs-v1 | 0 6 KB ggd-genomics
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The following NEW packages will be INSTALLED:
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hg19-gaps: 1-0 ggd-genomics
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hg19-gaps-ucsc-v1: 1-0 ggd-genomics
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Downloading and Extracting Packages
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hg19-gaps-1 | 6 KB | ####################### | 100%
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hg19-gaps-ucsc-v1 | 6 KB | ####################### | 100%
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Preparing transaction: done
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Verifying transaction: done
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Executing transaction: done

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