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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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