Shayan Doust pushed to branch master at Debian Med / mindthegap
Commits:
171decd0 by Shayan Doust at 2020-06-21T17:38:24+01:00
Add missing (test) dependency and fix test
- - - - -
2 changed files:
- debian/control
- debian/patches/modify_tests_for_autopkgtest.patch
Changes:
=====================================
debian/control
=====================================
@@ -18,7 +18,7 @@ Package: mindthegap
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends},
- libgatbcore2
+ libgatbcore3
Description: performs detection and assembly of DNA insertion variants in NGS
read datasets
Designed to call insertions of any size, whether they are novel or
duplicated, homozygous or heterozygous in the donor genome. It takes as
@@ -33,7 +33,8 @@ Description: performs detection and assembly of DNA insertion
variants in NGS re
Package: mindthegap-examples
Architecture: all
Depends: ${misc:Depends},
- python3
+ python3,
+ bsdextrautils | bsdmainutils (<< 12.1.1~)
Recommends: mindthegap
Description: optional scripts and example resources for mindthegap
Designed to call insertions of any size, whether they are novel or
=====================================
debian/patches/modify_tests_for_autopkgtest.patch
=====================================
@@ -1,7 +1,7 @@
Description: Fix upstream pre-existing test scripts
This will ensure that autopkgtest can invoke these scripts. They need to be
modified to remove any mindthegap binary checks that the upstream author has
put in place as well as ensuring the script invokes the global MindTheGap
command
Author: Shayan Doust <[email protected]>
-Last-Update: 2019-07-09
+Last-Update: 2020-06-21
--- mindthegap.orig/test/simple_full_test.sh
+++ mindthegap/test/simple_full_test.sh
@@ -31,6 +31,15 @@ Last-Update: 2019-07-09
-${bindir}/MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq
-ref ../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1
2> /dev/null
+MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref
../data/reference.fasta -out $outputPrefix >$outputPrefix.out -nb-cores 1 2>
/dev/null
+
################################################################################
+ # we check the results
+@@ -77,7 +64,7 @@
+
################################################################################
+ # we launch the find module with bed option
+
################################################################################
+-${bindir}/MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq
-ref ../data/reference.fasta -bed ${goldPrefix}.bed -out ${outputPrefix}_bed
>${outputPrefix}_bed.out -nb-cores 1 2> /dev/null
++MindTheGap find -in ../data/reads_r1.fastq,../data/reads_r2.fastq -ref
../data/reference.fasta -bed ${goldPrefix}.bed -out ${outputPrefix}_bed
>${outputPrefix}_bed.out -nb-cores 1 2> /dev/null
+
################################################################################
# we check the results
@@ -121,7 +108,7 @@
View it on GitLab:
https://salsa.debian.org/med-team/mindthegap/-/commit/171decd0b1a305ab7492f915fd67a23c5572d545
--
View it on GitLab:
https://salsa.debian.org/med-team/mindthegap/-/commit/171decd0b1a305ab7492f915fd67a23c5572d545
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