Andreas Tille pushed to branch master at Debian Med / resfinder
Commits: 5982f45b by Andreas Tille at 2019-11-15T09:17:47Z Package only Python version, provide example data in examples package - - - - - 8 changed files: - + debian/README.Debian - debian/changelog - debian/control - − debian/install - debian/lintian-overrides - + debian/resfinder-example.install - + debian/resfinder.install - + debian/resfinder.links Changes: ===================================== debian/README.Debian ===================================== @@ -0,0 +1,21 @@ +resfinder for Debian +==================== + +Quoting the resfinder doc: + + The ResFinder service contains one perl script *resfinder.pl* which is the + script of the latest version of the ResFinder service. ResFinder identifies + acquired antimicrobial resistance genes in total or partial sequenced isolates + of bacteria. + + This repository also contains a python script *resfinder.py* which is a new version + of ResFinder, but not yet running on the CGE server. This program was added because + it uses a newer version of blastn, which, in contrary from the blastall version + that the perl script uses, is avail to download. + +The user who requested this package is just interested in the Python version of +redfinder thus only this script is packaged. + + + -- Andreas Tille <[email protected]> Thu, 07 Nov 2019 12:41:11 +0100 + ===================================== debian/changelog ===================================== @@ -1,6 +1,5 @@ resfinder (3.2-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) - TODO: Clarify relation between *.pl and *.py -- Andreas Tille <[email protected]> Thu, 07 Nov 2019 12:41:11 +0100 ===================================== debian/control ===================================== @@ -4,16 +4,16 @@ Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 12), - dh-python + dh-python, + python3 Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/resfinder Vcs-Git: https://salsa.debian.org/med-team/resfinder.git Homepage: https://bitbucket.org/genomicepidemiology/resfinder Package: resfinder -Architecture: any -Depends: ${perl:Depends}, - ${python3:Depends}, +Architecture: all +Depends: ${python3:Depends}, ${misc:Depends}, bioperl, ncbi-blast+-legacy @@ -27,3 +27,20 @@ Description: identifies acquired antimicrobial resistance genes from four different sequencing platforms. The method was evaluated on 1862 GenBank files containing 1411 different resistance genes, as well as on 23 de-novo-sequenced isolates. + +Package: resfinder-example +Architecture: all +Depends: ${misc:Depends}, +Recommends: resfinder +Description: identifies acquired antimicrobial resistance genes (example data) + ResFinder identifies acquired antimicrobial resistance genes in total or + partial sequenced isolates of bacteria. + . + ResFinder that uses BLAST for identification of acquired antimicrobial + resistance genes in whole-genome data. As input, the method can use both + pre-assembled, complete or partial genomes, and short sequence reads + from four different sequencing platforms. The method was evaluated on + 1862 GenBank files containing 1411 different resistance genes, as well + as on 23 de-novo-sequenced isolates. + . + This package contains example data to test resfinder. ===================================== debian/install deleted ===================================== @@ -1,2 +0,0 @@ -*.py /usr/bin -*.pl /usr/bin ===================================== debian/lintian-overrides ===================================== @@ -1,4 +1,4 @@ # see discussion on Debian Med mailing list # https://lists.debian.org/debian-med/2018/06/msg00042.html # and following mails in thread -resfinder: script-with-language-extension usr/bin/resfinder.pl +resfinder: script-with-language-extension usr/bin/resfinder.py ===================================== debian/resfinder-example.install ===================================== @@ -0,0 +1 @@ +test.fsa usr/share/doc/resfinder/examples ===================================== debian/resfinder.install ===================================== @@ -0,0 +1 @@ +*.py usr/share/resfinder ===================================== debian/resfinder.links ===================================== @@ -0,0 +1 @@ +usr/share/resfinder/resfinder.py usr/bin/resfinder.py View it on GitLab: https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6 -- View it on GitLab: https://salsa.debian.org/med-team/resfinder/commit/5982f45bae1ad4f3e76e2ceb99f4e34b2bb0d4b6 You're receiving this email because of your account on salsa.debian.org.
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