Dropseq tools (#10170)

* first attempt

* package name now lowercase

* test command gave an exit 1

* another try

* try..

* missed a slash

* wrong test to test

* qutoe

* finalizing recipe before push

* last test

* add a test on help

* added test for each command

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
+

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`