Steffen Möller pushed to branch master at Debian Med / quast
Commits: 4ad40d3f by Steffen Moeller at 2021-08-25T01:16:16+02:00 Working on lintian erros - tests seem fine - - - - - 4 changed files: - debian/changelog - debian/control - + debian/quast.links - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,6 +1,21 @@ quast (5.0.2+dfsg-1) UNRELEASED; urgency=medium * Initial release (Closes: #963618) - * Builds, but tests fail - see d/TODO + * Seems fine, only some Lintian errors for embedded JavaScript need to be + addressed: +E: quast source: source-is-missing quast_libs/html_saver/static/bootstrap/bootstrap-tooltip-5px-lower.min.js +E: quast source: source-is-missing quast_libs/html_saver/static/bootstrap/bootstrap.min.js +E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.js line length is 2964 characters (>512) +E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.navigate.js line length is 1984 characters (>512) +E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.pie.js line length is 259 characters (>256) +E: quast source: source-is-missing quast_libs/html_saver/static/flot/jquery.flot.resize.js line length is 863 characters (>512) +E: quast source: source-is-missing quast_libs/html_saver/static/ie_html5.js line length is 2252 characters (>512) +E: quast source: source-is-missing quast_libs/html_saver/static/jquery-1.7.2.min.js +W: quast: embedded-javascript-library usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery.css please use libjs-jquery +W: quast: no-manual-page usr/bin/icarus.py +W: quast: no-manual-page usr/bin/metaquast.py +W: quast: no-manual-page usr/bin/quast-lg.py +W: quast: no-manual-page usr/bin/quast.py + -- Andreas Tille <[email protected]> Wed, 22 Apr 2020 15:30:18 +0200 ===================================== debian/control ===================================== @@ -17,7 +17,6 @@ Build-Depends: debhelper-compat (= 13), # hmmer, # bwa, # bedtools, -# busco, # ncbi-blast+, # sambamba Standards-Version: 4.5.0 @@ -45,7 +44,10 @@ Depends: ${shlibs:Depends}, busco, tigr-glimmer, python-matplotlib, - python3-joblib + python3-joblib, + libjs-excanvas, + libjs-jquery, + libjs-jquery-ui Description: Quality Assessment Tool for Genome Assemblies QUAST evaluates genome assemblies. For metagenomes, please see MetaQUAST project. It works both with and without a given reference genome. ===================================== debian/quast.links ===================================== @@ -0,0 +1,8 @@ +usr/share/javascript/excanvas/excanvas.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/excanvas.js +usr/share/javascript/excanvas/excanvas.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/excanvas.min.js +usr/share/javascript/jquery/jquery.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/jquery.js +usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/flot/jquery.min.js +usr/share/javascript/jquery-ui/ui/jquery-1-7.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.7.2.min.js +usr/share/javascript/jquery/jquery.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.8.2.js +usr/share/javascript/jquery/jquery.min.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-1.8.2.min.js +usr/share/javascript/jquery-ui/jquery-ui.js usr/lib/python3/dist-packages/quast_libs/html_saver/static/jquery-ui.js ===================================== debian/rules ===================================== @@ -1,19 +1,10 @@ #!/usr/bin/make -f -# DH_VERBOSE := 1 +DH_VERBOSE := 1 %: dh $@ --with python3 --buildsystem=pybuild -override_dh_auto_clean: - dh_auto_clean - rm -f quast_libs/busco/hmmsearch - find quast_libs -name "*.o" -delete - rm -f quast_libs/glimmer/glimmerhmm quast_libs/glimmer/src/make.err quast_libs/glimmer/src/make.log - rm -f quast_libs/version.py - # files generated while testing - rm -f quast_test_output/quast.log quast_test_output/quast_corrected_input/contigs_1.fasta quast_test_output/quast_corrected_input/contigs_2.fasta quast_test_output/quast_corrected_input/reference.fasta - override_dh_install: dh_install find debian -name LICENSE.txt -delete @@ -22,3 +13,22 @@ override_dh_auto_test: ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) PATH=$PATH:. ./setup.py test endif + +override_dh_auto_clean: + dh_auto_clean + rm -rf quast_test_output + rm -f quast_libs/busco/hmmsearch + find quast_libs -name "*.o" -delete + rm -f quast_libs/glimmer/glimmerhmm quast_libs/glimmer/src/make.err quast_libs/glimmer/src/make.log + rm -f quast_libs/version.py + #$(MAKE) -C quast_libs/MUMmer/ clean >/dev/null 2>/dev/null + rm -f quast_libs/MUMmer/make.* + #$(MAKE) -C quast_libs/glimmer/src/ clean >/dev/null 2>/dev/null + rm -f quast_libs/glimmer/src/make.* + rm -f *.pyc + rm -f quast_libs/*.pyc + rm -f quast_libs/html_saver/*.pyc + rm -f quast_libs/site_packages/*/*.pyc + #$(MAKE) -C quast_libs/bwa clean >/dev/null 2>/dev/null + rm -rf quast_libs/gridss* + rm -rf quast_libs/blast View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215 -- View it on GitLab: https://salsa.debian.org/med-team/quast/-/commit/4ad40d3fbf2fe943311d95ebb2b6c8c098763215 You're receiving this email because of your account on salsa.debian.org.
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