diff --git a/recipes/Drop-seq_tools/build.sh b/recipes/Drop-seq_tools/build.sh new file mode 100644 index 0000000000000..9b7e0f216d405 --- /dev/null +++ b/recipes/Drop-seq_tools/build.sh @@ -0,0 +1,43 @@ +#!/bin/bash +set -eu -o pipefail + +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' +) + +outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $outdir +bindir=$PREFIX/bin +mkdir -p $bindir +cp -r ./* $outdir/ + +for PROG in "${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 + diff --git a/recipes/Drop-seq_tools/meta.yaml b/recipes/Drop-seq_tools/meta.yaml new file mode 100644 index 0000000000000..446a80d2e967e --- /dev/null +++ b/recipes/Drop-seq_tools/meta.yaml @@ -0,0 +1,54 @@ +{% set name = "Drop-seq_tools" %} +{% set version = "1.13" %} +{% set versiongrep = "1.13(7bed8f4_1513008033)" %} + +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 }} + +build: + number: 0 + +source: + url: http://mccarrolllab.com/download/1276/{{ name }}-{{ version }}.zip + md5: 28533edd82867ed75867b05785cf8834 + +requirements: + run: + - openjdk >=7 + +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 }}"' + +extra: + notes: | + Drop-seq_tools utilities are wrapper shell scripts. To get help on individual tool, use e.g. `PolyATrimmer -- --help` \ No newline at end of file