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plasmidid_1.6.3+dfsg-1_amd64.changes (click to toggle)
Format:1.8
Date:Fri, 26 Jun 2020 17:56:19 +0200
Source:plasmidid
Binary:plasmidid
Architecture:source all
Version:1.6.3+dfsg-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Steffen Moeller <moeller@debian.org>
Description:
plasmidid  - mapping-based, assembly-assisted plasmid identification tool
Closes:963758
Changes:
plasmidid (1.6.3+dfsg-1) unstable; urgency=medium

  * Initial release (Closes: #963758)

  * Tests fail, apparently because of prokka
    https://github.com/BU-ISCIII/plasmidID/issues/12
Files:
8ab36de65295c97a4d9674366b3ac3e0 2224 science optional plasmidid_1.6.3+dfsg-1.dsc
f8ac2a559c777531ecc662e6660aa894 84777540 science optional plasmidid_1.6.3+dfsg.orig.tar.xz
f214588b073c60948e0586523dc51325 4040 science optional plasmidid_1.6.3+dfsg-1.debian.tar.xz
820f572c2024e68fed7a474c1d66ed94 46060 science optional plasmidid_1.6.3+dfsg-1_all.deb
f2419739d249ad4effad5b292418fb52 11289 science optional plasmidid_1.6.3+dfsg-1_amd64.buildinfo
plasmidid_1.6.3+dfsg-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:plasmidid
Binary:plasmidid
Architecture:all
Version:1.6.3+dfsg-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Andreas Tille <tille@debian.org>, Steffen Moeller <moeller@debian.org>
Homepage:https://github.com/BU-ISCIII/plasmidID
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/plasmidid
Vcs-Git:https://salsa.debian.org/med-team/plasmidid.git
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>
Package-List:plasmidid deb science optional arch=all
Files:
f8ac2a559c777531ecc662e6660aa894 84777540 plasmidid_1.6.3+dfsg.orig.tar.xz
f214588b073c60948e0586523dc51325 4040 plasmidid_1.6.3+dfsg-1.debian.tar.xz
lintian 2.79.0~bpo10+1 check for plasmidid_1.6.3+dfsg-1.dsc (click to toggle)
README.source for plasmidid_1.6.3+dfsg-1.dsc (click to toggle)
No README.source in this package
control file for plasmidid_1.6.3+dfsg-1_all.deb (click to toggle)
Package:plasmidid
Version:1.6.3+dfsg-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:329
Depends:python3:any, ncbi-blast+, bedtools, bowtie2, samtools, prokka, cd-hit, mash, circos
Recommends:trimmomatic, spades, python3-biopython, python3-numpy, python3-pandas
Section:science
Priority:optional
Homepage:https://github.com/BU-ISCIII/plasmidID
Description:
mapping-based, assembly-assisted plasmid identification tool
 PlasmidID is a mapping-based, assembly-assisted plasmid identification
 tool that analyzes and gives graphic solution for plasmid
 identification.
 .
 PlasmidID is a computational pipeline that maps Illumina reads over
 plasmid database sequences. The k-mer filtered, most covered
 sequences are clustered by identity to avoid redundancy and the
 longest are used as scaffold for plasmid reconstruction. Reads are
 assembled and annotated by automatic and specific annotation. All
 information generated from mapping, assembly, annotation and local
 alignment analyses is gathered and accurately represented in a
 circular image which allow user to determine plasmidic composition in
 any bacterial sample.
lintian 2.79.0~bpo10+1 check for plasmidid_1.6.3+dfsg-1_all.deb (click to toggle)
contents of plasmidid_1.6.3+dfsg-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-06-26 15:56 ./
drwxr-xr-x root/root         0 2020-06-26 15:56 ./etc/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./etc/plasmidid/
-rw-r--r-- root/root      8884 2020-06-16 12:00 ./etc/plasmidid/OR.conf
-rw-r--r-- root/root      8648 2020-06-16 12:00 ./etc/plasmidid/circos_individual_1_3_0.conf
-rw-r--r-- root/root      9467 2020-06-16 12:00 ./etc/plasmidid/circos_individual_1_3_3.conf
-rw-r--r-- root/root      7160 2020-06-16 12:00 ./etc/plasmidid/circos_summary_1_3_0.conf
-rw-r--r-- root/root      7646 2020-06-16 12:00 ./etc/plasmidid/circos_summary_1_3_3.conf
-rw-r--r-- root/root      6516 2020-06-16 12:00 ./etc/plasmidid/simple.conf
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/bin/
-rwxr-xr-x root/root       176 2020-06-26 15:56 ./usr/bin/plasmidID
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/doc/plasmidid/
-rw-r--r-- root/root       233 2020-06-26 15:56 ./usr/share/doc/plasmidid/changelog.Debian.gz
-rw-r--r-- root/root      1326 2020-06-16 12:00 ./usr/share/doc/plasmidid/changelog.gz
-rw-r--r-- root/root      1210 2020-06-26 15:56 ./usr/share/doc/plasmidid/copyright
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/man/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/man/man1/
-rw-r--r-- root/root      1650 2020-06-26 15:56 ./usr/share/man/man1/plasmidID.1.gz
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/plasmidid/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/plasmidid/bin/
-rwxr-xr-x root/root      5135 2020-06-16 12:00 ./usr/share/plasmidid/bin/adapt_filter_coverage.sh
-rwxr-xr-x root/root      6411 2020-06-16 12:00 ./usr/share/plasmidid/bin/blast_align.sh
-rwxr-xr-x root/root      7579 2020-06-16 12:00 ./usr/share/plasmidid/bin/blast_to_bed.sh
-rwxr-xr-x root/root      8335 2020-06-16 12:00 ./usr/share/plasmidid/bin/blast_to_complete.sh
-rwxr-xr-x root/root      7223 2020-06-16 12:00 ./usr/share/plasmidid/bin/blast_to_link.sh
-rwxr-xr-x root/root      5169 2020-06-16 12:00 ./usr/share/plasmidid/bin/bowtie_mapper.sh
-rwxr-xr-x root/root      6401 2020-06-16 12:00 ./usr/share/plasmidid/bin/build_karyotype.sh
-rwxr-xr-x root/root      4083 2020-06-16 12:00 ./usr/share/plasmidid/bin/calculate_seqlen.sh
-rwxr-xr-x root/root      7985 2020-06-16 12:00 ./usr/share/plasmidid/bin/cdhit_cluster.sh
-rwxr-xr-x root/root      1724 2020-06-16 12:00 ./usr/share/plasmidid/bin/check_dependencies.sh
-rwxr-xr-x root/root      1044 2020-06-16 12:00 ./usr/share/plasmidid/bin/check_mandatory_files.sh
-rwxr-xr-x root/root      6868 2020-06-16 12:00 ./usr/share/plasmidid/bin/coordinate_adapter.sh
-rwxr-xr-x root/root      5372 2020-06-26 15:56 ./usr/share/plasmidid/bin/download_plasmid_database.py
-rwxr-xr-x root/root      7978 2020-06-16 12:00 ./usr/share/plasmidid/bin/draw_circos_images.sh
-rwxr-xr-x root/root      7349 2020-06-16 12:00 ./usr/share/plasmidid/bin/filter_fasta.sh
-rwxr-xr-x root/root      6105 2020-06-16 12:00 ./usr/share/plasmidid/bin/get_coverage.sh
-rwxr-xr-x root/root      8823 2020-06-16 12:00 ./usr/share/plasmidid/bin/gff_to_bed.sh
-rwxr-xr-x root/root      5319 2020-06-16 12:00 ./usr/share/plasmidid/bin/mash_screener.sh
-rwxr-xr-x root/root     15583 2020-06-26 15:56 ./usr/share/plasmidid/bin/mashclust.py
-rwxr-xr-x root/root      6635 2020-06-16 12:00 ./usr/share/plasmidid/bin/ncbi_database_fetcher.sh
-rwxr-xr-x root/root      5247 2020-06-16 12:00 ./usr/share/plasmidid/bin/process_cluster_output.sh
-rwxr-xr-x root/root      4981 2020-06-16 12:00 ./usr/share/plasmidid/bin/prokka_annotation.sh
-rwxr-xr-x root/root      5097 2020-06-16 12:00 ./usr/share/plasmidid/bin/quality_trim.sh
-rwxr-xr-x root/root      5544 2020-06-16 12:00 ./usr/share/plasmidid/bin/rename_from_fasta.sh
-rwxr-xr-x root/root      5241 2020-06-16 12:00 ./usr/share/plasmidid/bin/sam_to_bam.sh
-rwxr-xr-x root/root      5524 2020-06-16 12:00 ./usr/share/plasmidid/bin/spades_assembly.sh
-rwxr-xr-x root/root     15033 2020-06-26 15:56 ./usr/share/plasmidid/bin/summary_report_pid.py
-rwxr-xr-x root/root     15093 2020-06-16 12:00 ./usr/share/plasmidid/bin/summary_table.sh
-rwxr-xr-x root/root     48494 2020-06-26 15:56 ./usr/share/plasmidid/plasmidID
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/python3/
drwxr-xr-x root/root         0 2020-06-26 15:56 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root       141 2020-06-26 15:56 ./usr/share/python3/runtime.d/plasmidid.rtupdate

Timestamp: 26.06.2020 / 22:01:27 (UTC)