[med-svn] [Git][med-team/mindthegap][master] Add missing (test) dependency and fix test

[Shayan Doust]

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 <hello at shayandoust.me>
-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

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View it on GitLab: https://salsa.debian.org/med-team/mindthegap/-/commit/171decd0b1a305ab7492f915fd67a23c5572d545
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