[med-svn] [Git][med-team/drop-seq][master] 5 commits: Link to excluded file
Pranav Ballaney
gitlab at salsa.debian.org
Tue Jun 16 17:28:28 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / drop-seq
Commits:
5df8913e by Pranav Ballaney at 2020-06-16T15:20:14+05:30
Link to excluded file
- - - - -
bcb673f2 by Pranav Ballaney at 2020-06-16T20:36:35+05:30
Install scripts that come with this package
- - - - -
8f3db984 by Pranav Ballaney at 2020-06-16T20:37:01+05:30
Install reference data
- - - - -
b85b04a2 by Pranav Ballaney at 2020-06-16T20:37:15+05:30
Add autopkgtests
- - - - -
7203c8e0 by Pranav Ballaney at 2020-06-16T20:40:43+05:30
Install docs
- - - - -
15 changed files:
- + debian/README.test
- debian/changelog
- + debian/docs
- debian/drop-seq-testdata.install
- debian/drop-seq-tools.install
- + debian/patches/link_excluded_file.patch
- debian/patches/series
- + debian/tests/control
- + debian/tests/ref/FilterBam.sam
- + debian/tests/ref/PolyATrimmer.sam
- + debian/tests/ref/README.test_data
- + debian/tests/ref/TagBamWithReadSequenceExtended-cellular.sam
- + debian/tests/ref/TagBamWithReadSequenceExtended-molecular.sam
- + debian/tests/ref/TrimStartingSequence.sam
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+drop-seq (2.3.0+dfsg-3) UNRELEASED; urgency=medium
+
+ * Link to excluded file
+ * Install scripts that come with this package
+ * Install reference data
+ * Add autopkgtests
+ * Install docs
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Tue, 16 Jun 2020 20:37:20 +0530
+
drop-seq (2.3.0+dfsg-2) unstable; urgency=medium
* debhelper-compat 13 (routine-update)
=====================================
debian/docs
=====================================
@@ -0,0 +1,4 @@
+README.md
+debian/README*
+debian/tests/run-unit-test
+debian/tests/ref/README*
\ No newline at end of file
=====================================
debian/drop-seq-testdata.install
=====================================
@@ -1 +1,2 @@
-testdata/* usr/share/drop-seq
+testdata/* usr/share/doc/drop-seq/examples/
+debian/tests/ref usr/share/doc/drop-seq/examples/
\ No newline at end of file
=====================================
debian/drop-seq-tools.install
=====================================
@@ -1 +1,2 @@
debian/bin usr
+src/scripts/* usr/bin/
=====================================
debian/patches/link_excluded_file.patch
=====================================
@@ -0,0 +1,10 @@
+--- a/README.md
++++ b/README.md
+@@ -6,4 +6,4 @@ You may also use this address to be adde
+
+ See https://github.com/broadinstitute/Drop-seq/releases to download binaries.
+
+-See [Drop-seq alignment cookbook](doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.
+\ No newline at end of file
++See [Drop-seq alignment cookbook](https://github.com/broadinstitute/Drop-seq/blob/master/doc/Drop-seq_Alignment_Cookbook.pdf) for detailed usage of these tools.
+\ No newline at end of file
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
no_git.patch
debian_packaged_libs.patch
+link_excluded_file.patch
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, samtools
+Restrictions: allow-stderr
=====================================
debian/tests/ref/FilterBam.sam
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/ref/PolyATrimmer.sam
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/ref/README.test_data
=====================================
@@ -0,0 +1,2 @@
+The files used as references for testing were obtained by running the software on
+the data provided in the testdata folder with this package.
\ No newline at end of file
=====================================
debian/tests/ref/TagBamWithReadSequenceExtended-cellular.sam
=====================================
@@ -0,0 +1,5 @@
+000000000-AMY9M:1:1111:13708:20052 0 1 565193 3 24M * 0 0 GTATTTCCTCACGCAAGCAACCGC BBBBBFDFFFFAGG?EGGGGCFEC XC:Z:GTATTTCCTCAC MD:Z:24 XF:Z:INTERGENIC PG:Z:STAR RG:Z:00000.1 XG:Z:RP5-857K21.4 NH:i:2 NM:i:0 XM:Z:CTAATATG ZP:i:25 UQ:i:0 AS:i:23 gf:Z:INTRONIC gn:Z:RP5-857K21.4 gs:Z:-
+000000000-AMY9M:1:2104:20987:12124 16 1 6246604 1 50M * 0 0 GGAAGCCCTTTGACTATGATTTCCAATTTTCTGTTCAATCCACACTGCAG HHGCFAHFGDHGGHHGHGHHHHGGHHHHFGGGGGGFGGBBFFFFF3BBBA XC:Z:GGAAGCCCTTTG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:RPL22 NH:i:3 NM:i:0 XM:Z:GTTGGGCC UQ:i:0 AS:i:49 gf:Z:CODING,UTR gn:Z:RPL22,RPL22 gs:Z:-,-
+000000000-AMY9M:1:1114:17300:12082 0 1 16058910 255 50M * 0 0 CCTCTTTACGTGCCATGAGGATTGCCAGACCAGCTTCTTCCGCTCTTTGG BBBBBFFFFACFFGGGGGCGGFDGGHH4GGHHFHHFHHHHHDG2EHFGG3 XC:Z:CCTCTTTACGTG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:AAGACCAC UQ:i:0 AS:i:49 gf:Z:CODING,CODING gn:Z:PLEKHM2,RP11-288I21.1 gs:Z:+,-
+000000000-AMY9M:1:2104:15433:7166 0 1 16059019 255 6M82N44M * 0 0 GTCTTGGAGTTCTCCCAGGACAGCCAGCAGCTCCTCCCGCCCTGGGTCAT AAABBFFFBCCFGGGGGGCGGGAGHHHGHHHHHGHHHGGGGGGHHAGGAG XC:Z:GTCTTGGAGTTC MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:AAGACCAC UQ:i:0 AS:i:50 gf:Z:CODING,CODING,INTRONIC gn:Z:PLEKHM2,RP11-288I21.1,RP11-288I21.1 gs:Z:+,-,-
+000000000-AMY9M:1:2109:19958:23569 0 1 38484134 255 12S38M * 0 0 GGGTTAAACTCCAGGCTGGAGTACATATTATTAAGGAGACTAAGGAAGAA ?AAAAA1DFFFFF1C1AAE1GGGHHHBGB33GAE1G1BGEBGFHGGB0GH XC:Z:GGGTTAAACTCC MD:Z:3A34 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:UTP11L NH:i:1 NM:i:1 XM:Z:GGGAGTCG UQ:i:16 AS:i:35 gf:Z:CODING,INTRONIC gn:Z:UTP11L,UTP11L gs:Z:+,+
=====================================
debian/tests/ref/TagBamWithReadSequenceExtended-molecular.sam
=====================================
@@ -0,0 +1,5 @@
+000000000-AMY9M:1:1111:13708:20052 0 1 565193 3 24M * 0 0 GTATTTCCTCACGCAAGCAACCGC BBBBBFDFFFFAGG?EGGGGCFEC XC:Z:CGCCTCCTCCGA MD:Z:24 XF:Z:INTERGENIC PG:Z:STAR RG:Z:00000.1 XG:Z:RP5-857K21.4 NH:i:2 NM:i:0 XM:Z:GTATTTCCTCAC ZP:i:25 UQ:i:0 AS:i:23 gf:Z:INTRONIC gn:Z:RP5-857K21.4 gs:Z:-
+000000000-AMY9M:1:2104:20987:12124 16 1 6246604 1 50M * 0 0 GGAAGCCCTTTGACTATGATTTCCAATTTTCTGTTCAATCCACACTGCAG HHGCFAHFGDHGGHHGHGHHHHGGHHHHFGGGGGGFGGBBFFFFF3BBBA XC:Z:TGGCTGTTCTTT MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:RPL22 NH:i:3 NM:i:0 XM:Z:GGAAGCCCTTTG UQ:i:0 AS:i:49 gf:Z:CODING,UTR gn:Z:RPL22,RPL22 gs:Z:-,-
+000000000-AMY9M:1:1114:17300:12082 0 1 16058910 255 50M * 0 0 CCTCTTTACGTGCCATGAGGATTGCCAGACCAGCTTCTTCCGCTCTTTGG BBBBBFFFFACFFGGGGGCGGFDGGHH4GGHHFHHFHHHHHDG2EHFGG3 XC:Z:AGTGAGACAAGG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:CCTCTTTACGTG UQ:i:0 AS:i:49 gf:Z:CODING,CODING gn:Z:PLEKHM2,RP11-288I21.1 gs:Z:+,-
+000000000-AMY9M:1:2104:15433:7166 0 1 16059019 255 6M82N44M * 0 0 GTCTTGGAGTTCTCCCAGGACAGCCAGCAGCTCCTCCCGCCCTGGGTCAT AAABBFFFBCCFGGGGGGCGGGAGHHHGHHHHHGHHHGGGGGGHHAGGAG XC:Z:AGTGAGACAAGG MD:Z:50 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:PLEKHM2,RP11-288I21.1 NH:i:1 NM:i:0 XM:Z:GTCTTGGAGTTC UQ:i:0 AS:i:50 gf:Z:CODING,CODING,INTRONIC gn:Z:PLEKHM2,RP11-288I21.1,RP11-288I21.1 gs:Z:+,-,-
+000000000-AMY9M:1:2109:19958:23569 0 1 38484134 255 12S38M * 0 0 GGGTTAAACTCCAGGCTGGAGTACATATTATTAAGGAGACTAAGGAAGAA ?AAAAA1DFFFFF1C1AAE1GGGHHHBGB33GAE1G1BGEBGFHGGB0GH XC:Z:AGTGAGACAAGG MD:Z:3A34 XF:Z:CODING PG:Z:STAR RG:Z:00000.1 XG:Z:UTP11L NH:i:1 NM:i:1 XM:Z:GGGTTAAACTCC UQ:i:16 AS:i:35 gf:Z:CODING,INTRONIC gn:Z:UTP11L,UTP11L gs:Z:+,+
=====================================
debian/tests/ref/TrimStartingSequence.sam
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,65 @@
+#!/bin/bash
+set -e
+
+pkg=drop-seq
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ # Double quote below to expand the temporary directory variable now versus
+ # later is on purpose.
+ # shellcheck disable=SC2064
+ trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+# gunzip -r mm10/*
+gunzip -r ref/*
+gunzip -r org/broadinstitute/dropseq/annotation/*
+gunzip -r org/broadinstitute/dropseq/readtrimming/*
+mkdir out
+#do_stuff_to_test_package#
+
+echo -e "\e[93m\e[1mTest 1\e[0m"
+drop-seq TagBamWithReadSequenceExtended INPUT=org/broadinstitute/dropseq/annotation/test.bam \
+ OUTPUT=out/TagBamWithReadSequenceExtended-cellular.bam SUMMARY=TagBamWithReadSequenceExtended-cellular.bam_summary.txt BASE_RANGE=1-12 BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=false TAG_NAME=XC NUM_BASES_BELOW_QUALITY=1
+samtools view out/TagBamWithReadSequenceExtended-cellular.bam > out/TagBamWithReadSequenceExtended-cellular.sam
+diff out/TagBamWithReadSequenceExtended-cellular.sam ref/TagBamWithReadSequenceExtended-cellular.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+drop-seq TagBamWithReadSequenceExtended INPUT=org/broadinstitute/dropseq/annotation/test.bam \
+ OUTPUT=out/TagBamWithReadSequenceExtended-molecular.bam SUMMARY=TagBamWithReadSequenceExtended-molecular.bam_summary.txt BASE_RANGE=1-12 BASE_QUALITY=10 BARCODED_READ=1 DISCARD_READ=false TAG_NAME=XM NUM_BASES_BELOW_QUALITY=1
+samtools view out/TagBamWithReadSequenceExtended-molecular.bam > out/TagBamWithReadSequenceExtended-molecular.sam
+diff out/TagBamWithReadSequenceExtended-molecular.sam ref/TagBamWithReadSequenceExtended-molecular.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+drop-seq FilterBam TAG_REJECT=XQ INPUT=org/broadinstitute/dropseq/readtrimming/N701.subset.tagged_filtered.sam \
+ OUTPUT=out/FilterBam.bam
+samtools view out/FilterBam.bam > out/FilterBam.sam
+diff out/FilterBam.sam ref/FilterBam.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+drop-seq TrimStartingSequence INPUT=out/FilterBam.bam OUTPUT=out/TrimStartingSequence.bam \
+ OUTPUT_SUMMARY=out/TrimStartingSequence.summary.txt SEQUENCE=AAGCAGTGGTATCAACGCAGAGTGAATGGG MISMATCHES=0 NUM_BASES=5
+samtools view out/TrimStartingSequence.bam > out/TrimStartingSequence.sam
+diff out/TrimStartingSequence.sam ref/TrimStartingSequence.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5\e[0m"
+drop-seq PolyATrimmer INPUT=out/TrimStartingSequence.bam OUTPUT=out/PolyATrimmer.bam \
+ OUTPUT_SUMMARY=out/PolyATrimmer.summary.bam MISMATCHES=0 NUM_BASES=6 USE_NEW_TRIMMER=true
+samtools view out/PolyATrimmer.bam > out/PolyATrimmer.sam
+diff out/PolyATrimmer.sam ref/PolyATrimmer.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7
--
View it on GitLab: https://salsa.debian.org/med-team/drop-seq/-/compare/b2cecbee9024528a5825c8f274285e240894ab44...7203c8e0e5ad7b5ba74bbaa447fc2ab3784516f7
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