[med-svn] [Git][med-team/plasmidid][master] Added tests

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / plasmidid


Commits:
c218fc28 by Steffen Moeller at 2020-06-26T19:12:34+02:00
Added tests

Failure reported as https://github.com/BU-ISCIII/plasmidID/issues/12

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/patches/config_files.patch
- + debian/patches/fixTests.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -9,5 +9,7 @@ plasmidid (1.6.3+dfsg-1) UNRELEASED; urgency=medium
   * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
     Repository-Browse. (routine-update)
   * Employ help2man to create missing man page
+  * Tests fail, apparently because of prokka
+    https://github.com/BU-ISCIII/plasmidID/issues/12
 
  -- Steffen Moeller <moeller at debian.org>  Fri, 26 Jun 2020 17:56:19 +0200


=====================================
debian/control
=====================================
@@ -8,6 +8,14 @@ Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3-all,
                help2man
+               ncbi-blast+ <!nocheck>,
+               bedtools <!nocheck>,
+               bowtie2 <!nocheck>,
+               samtools <!nocheck>,
+               prokka <!nocheck>,
+               cd-hit <!nocheck>,
+               mash <!nocheck>,
+               circos <!nocheck>
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/plasmidid
 Vcs-Git: https://salsa.debian.org/med-team/plasmidid.git
@@ -25,6 +33,7 @@ Depends: ${misc:Depends},
          samtools,
          prokka,
          cd-hit,
+         mash,
          circos
 Recommends: trimmomatic,
             spades,


=====================================
debian/patches/config_files.patch
=====================================
@@ -1,15 +0,0 @@
-Index: plasmidid/plasmidID
-===================================================================
---- plasmidid.orig/plasmidID
-+++ plasmidid/plasmidID
-@@ -190,8 +190,8 @@ annotation=false
- verbose_option_circos=""
- w_winner="-w"
- is_verbose=false
--config_dir="$script_dir/config_files"
--trimmomatic_directory=/opt/Trimmomatic/
-+config_dir="/etc/plasmidid"
-+trimmomatic_directory=/usr/share/java/
- config_file_individual="circos_individual_1_3_3.conf"
- #SET COLORS
- 


=====================================
debian/patches/fixTests.patch
=====================================
@@ -0,0 +1,22 @@
+Index: plasmidid/TEST_DATA/test.sh
+===================================================================
+--- plasmidid.orig/TEST_DATA/test.sh
++++ plasmidid/TEST_DATA/test.sh
+@@ -127,7 +127,7 @@ done
+ shift $((OPTIND-1))
+ 
+ ## Execute plasmidID with test data.
+-echo "Executing:../plasmidID.sh -1 $R1 -2 $R2 -d $database -c $contigs -s KPN --no-trim"
++echo "Executing:../plasmidID -1 $R1 -2 $R2 -d $database -c $contigs -s KPN --no-trim"
+ echo "Forward reads: $R1"
+ echo "Reverse reads: $R2"
+ echo "PlasmidDatabase: $database"
+@@ -136,7 +136,7 @@ echo "Options: --no-trim"
+ 
+ echo "export PATH=$PATH:$script_dir/../bin" > path
+ source path
+-$script_dir/../plasmidID.sh -1 $script_dir/$R1 -2 $script_dir/$R2 -d $script_dir/$database -c $script_dir/$contigs -s KPN --no-trim
++$script_dir/../plasmidID -1 $script_dir/$R1 -2 $script_dir/$R2 -d $script_dir/$database -c $script_dir/$contigs -s KPN --no-trim
+ 
+ 
+ echo "ALL DONE. TEST COMPLETED SUCCESSFULLY YOUR INSTALLATION SHOULD BE CORRECT."


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
 config_files.patch
+fixTests.patch
 AdjustPythonPath.patch


=====================================
debian/rules
=====================================
@@ -12,6 +12,12 @@ override_dh_auto_install:
 	dh_auto_install
 	help2man -i debian/plasmidID.h2m ./plasmidID > debian/plasmidID.1
 
+override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
+	PATH=$$PATH:$(CURDIR)/bin TEST_DATA/test.sh || true
+endif
+
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f debian/plasmidID.1
+	rm -rf NO_GROUP/ TEST_DATA/plasmids_TEST_database.fasta.length TEST_DATA/plasmids_TEST_database.length debian/patches/fixTest.patch path



View it on GitLab: https://salsa.debian.org/med-team/plasmidid/-/commit/c218fc2844b214418a589bba99b80bd743115a7b

-- 
View it on GitLab: https://salsa.debian.org/med-team/plasmidid/-/commit/c218fc2844b214418a589bba99b80bd743115a7b
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