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Dropseq tools #10170
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Dropseq tools #10170
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9971eb0
first attempt
cgirardot 4b5e11c
package name now lowercase
cgirardot eb26828
test command gave an exit 1
cgirardot f786d51
another try
cgirardot 47448ee
try..
cgirardot 56991a1
missed a slash
cgirardot 0179119
wrong test to test
cgirardot c33bfa6
qutoe
cgirardot 4e59120
finalizing recipe before push
cgirardot d9f672b
last test
cgirardot 136ac12
add a test on help
cgirardot 64cf532
added test for each command
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Original file line number | Diff line number | Diff line change |
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#!/bin/bash | ||
set -eu -o pipefail | ||
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declare -a PROGRAMS=( | ||
'BAMTagHistogram' | ||
'BAMTagofTagCounts' | ||
'BaseDistributionAtReadPosition' | ||
'CollapseBarcodesInPlace' | ||
'CollapseTagWithContext' | ||
'ConvertToRefFlat' | ||
'CreateIntervalsFiles' | ||
'DetectBeadSynthesisErrors' | ||
'DigitalExpression' | ||
'FilterBAM' | ||
'FilterBAMByTag' | ||
'GatherGeneGCLength' | ||
'GatherMolecularBarcodeDistributionByGene' | ||
'GatherReadQualityMetrics' | ||
'PolyATrimmer' | ||
'ReduceGTF' | ||
'SelectCellsByNumTranscripts' | ||
'SingleCellRnaSeqMetricsCollector' | ||
'TagBamWithReadSequenceExtended' | ||
'TagReadWithGeneExon' | ||
'TagReadWithInterval' | ||
'TrimStartingSequence' | ||
'ValidateReference' | ||
) | ||
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||
outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM | ||
mkdir -p $outdir | ||
bindir=$PREFIX/bin | ||
mkdir -p $bindir | ||
cp -r ./* $outdir/ | ||
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||
for PROG in "${PROGRAMS[@]}" | ||
do | ||
sed -i'.bak' -E 's@^thisdir=.+@thisdir='$outdir'@g' "${outdir}/${PROG}" | ||
rm -f "${outdir}/${PROG}.bak" | ||
ln -s "${outdir}/${PROG}" "${bindir}/${PROG}" | ||
chmod 0755 "${bindir}/${PROG}" | ||
done | ||
|
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{% set name = "Drop-seq_tools" %} | ||
{% set version = "1.13" %} | ||
{% set versiongrep = "1.13(7bed8f4_1513008033)" %} | ||
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about: | ||
home: http://mccarrolllab.com/dropseq/ | ||
license: MIT License | ||
license_family: MIT | ||
summary: | | ||
Package fot the analysis of Drop-seq data developed by Jim Nemesh in the McCarroll Lab | ||
package: | ||
name: dropseq_tools | ||
version: {{ version }} | ||
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build: | ||
number: 0 | ||
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source: | ||
url: http://mccarrolllab.com/download/1276/{{ name }}-{{ version }}.zip | ||
md5: 28533edd82867ed75867b05785cf8834 | ||
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requirements: | ||
run: | ||
- openjdk >=7 | ||
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test: | ||
commands: | ||
- 'BAMTagHistogram -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'BAMTagofTagCounts -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'BaseDistributionAtReadPosition -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'CollapseBarcodesInPlace -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'CollapseTagWithContext -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'ConvertToRefFlat -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'CreateIntervalsFiles -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'DetectBeadSynthesisErrors -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'DigitalExpression -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'FilterBAM -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'FilterBAMByTag -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'GatherGeneGCLength -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'GatherMolecularBarcodeDistributionByGene -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'GatherReadQualityMetrics -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'PolyATrimmer -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'ReduceGTF -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'SelectCellsByNumTranscripts -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'SingleCellRnaSeqMetricsCollector -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'TagBamWithReadSequenceExtended -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'TagReadWithGeneExon -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'TagReadWithInterval -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'TrimStartingSequence -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
- 'ValidateReference -- --help 2>&1 | grep "{{ versiongrep }}"' | ||
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extra: | ||
notes: | | ||
Drop-seq_tools utilities are wrapper shell scripts. To get help on individual tool, use e.g. `PolyATrimmer -- --help` |
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Can we have small letters here?
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the name is used to build the file name to download from their web site. I'd rather keep it like this if possible.