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seqkit_0.12.1+ds-1_amd64.changes (click to toggle)
Format:1.8
Date:Mon, 03 Aug 2020 21:49:28 +0530
Source:seqkit
Binary:seqkit seqkit-examples
Architecture:source all amd64
Version:0.12.1+ds-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Nilesh Patra <npatra974@gmail.com>
Description:
seqkit     - cross-platform and ultrafast toolkit for FASTA/Q file manipulatio
seqkit-examples - examples for seqkit: toolkit for FASTA/Q file manipulation
Closes:967051
Changes:
seqkit (0.12.1+ds-1) unstable; urgency=medium

  * Initial release (Closes: #967051)
Files:
9a9a43d7991fbfa6fdd44d2ba25b4fcc 2729 science optional seqkit_0.12.1+ds-1.dsc
434a526394a160756467956df08cc826 12487112 science optional seqkit_0.12.1+ds.orig.tar.xz
21b4afa7e7e37582b94408c2064de2fa 10746360 science optional seqkit_0.12.1+ds-1.debian.tar.xz
b4460f7bdd2524dd40b9f8dd6ace771b 35791568 science optional seqkit-examples_0.12.1+ds-1_all.deb
c85b2f75a208495aee123b88b73f015f 10289 science optional seqkit_0.12.1+ds-1_amd64.buildinfo
09df4c707f47fb53107e7ecec4de86a6 6455784 science optional seqkit_0.12.1+ds-1_amd64.deb
seqkit_0.12.1+ds-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:seqkit
Binary:seqkit, seqkit-examples
Architecture:any all
Version:0.12.1+ds-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Andreas Tille <tille@debian.org>, Nilesh Patra <npatra974@gmail.com>
Homepage:https://github.com/shenwei356/seqkit
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/seqkit
Vcs-Git:https://salsa.debian.org/med-team/seqkit.git
Testsuite:autopkgtest
Build-Depends:debhelper-compat (=13), dh-golang, golang-any, golang-github-biogo-biogo-dev, golang-github-biogo-hts-dev, golang-github-bsipos-thist-dev, golang-github-cespare-xxhash-dev, golang-github-cznic-sortutil-dev, golang-github-dustin-go-humanize-dev, golang-github-fsnotify-fsnotify-dev, golang-github-logrusorgru-aurora-dev, golang-github-mattn-go-colorable-dev, golang-github-mattn-go-isatty-dev, golang-github-mitchellh-go-homedir-dev, golang-github-op-go-logging-dev, golang-github-shenwei356-bio-dev, golang-github-shenwei356-bwt-dev, golang-github-spf13-cobra-dev, golang-github-tatsushid-go-prettytable-dev, samtools
Package-List:seqkit deb science optional arch=any seqkit-examples deb science optional arch=all
Files:
434a526394a160756467956df08cc826 12487112 seqkit_0.12.1+ds.orig.tar.xz
21b4afa7e7e37582b94408c2064de2fa 10746360 seqkit_0.12.1+ds-1.debian.tar.xz
Go-Import-Path:github.com/shenwei356/seqkit
lintian 2.85.0~bpo10+1 check for seqkit_0.12.1+ds-1.dsc (click to toggle)
README.source for seqkit_0.12.1+ds-1.dsc (click to toggle)
Upstream provides binary files without sources for:

* tests/pcs109_5k_prim.sam 
* tests/pcs109_5k.sam
* tests/pcs109_5k_spliced.sam

These have been converted to corresponding text (.sam) files with command:
* samtools view -h -o <out>.sam <in>.bam 

And the corresponding *.sam files are added to: debian/missing-sources

They can be generated back with the following commands:
*	cat debian/missing-sources/pcs109_5k_prim.sam | samtools view -Sb - > tests/pcs109_5k_prim.bam
*	cat debian/missing-sources/pcs109_5k.sam | samtools view -Sb - > tests/pcs109_5k.bam
*	cat debian/missing-sources/pcs109_5k_spliced.sam | samtools view -Sb - > tests/pcs109_5k_spliced.bam
*	samtools index tests/pcs109_5k_prim.bam tests/pcs109_5k_prim.bam.bai
*	samtools index tests/pcs109_5k.bam tests/pcs109_5k.bam.bai
*	samtools index tests/pcs109_5k_spliced.bam tests/pcs109_5k_spliced.bam.bai

These commands are also being run in debian/rules since these binaries are needed for autopkgtests.

 -- Nilesh Patra <npatra974@gmail.com>  Mon, 03 Aug 2020 21:49:28 +0530

control file for seqkit_0.12.1+ds-1_amd64.deb (click to toggle)
Package:seqkit
Version:0.12.1+ds-1
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:16202
Depends:libc6 (>=2.4)
Built-Using:golang-1.14 (= 1.14.6-1), golang-github-ajstarks-svgo (= 2012-01-27-2), golang-github-biogo-biogo (= 1.0.2-2), golang-github-biogo-hts (= 1.1.0+dfsg1-2), golang-github-bsipos-thist (= 1.0.0-1), golang-github-cespare-xxhash (= 2.1.1-1), golang-github-cznic-sortutil (= 0.0~git20150617.0.4c73428-2), golang-github-dustin-go-humanize (= 1.0.0-1), golang-github-edsrzf-mmap-go (= 0.0~git20170320.0.0bce6a6-5), golang-github-fogleman-gg (= 1.3.0-1), golang-github-golang-freetype (= 0.0~git20170609.e2365df+dfsg-1), golang-github-jung-kurt-gofpdf (= 2.17.2+ds-2), golang-github-klauspost-compress (= 1.9.5-2), golang-github-klauspost-pgzip (= 1.2.1-1), golang-github-logrusorgru-aurora (= 2.0.3-1), golang-github-mattn-go-colorable (= 0.1.6-1), golang-github-mattn-go-isatty (= 0.0.12-1), golang-github-mattn-go-runewidth (= 0.0.9-1), golang-github-mitchellh-go-homedir (= 1.1.0-1), golang-github-op-go-logging (= 1+git20160315.970db52-2), golang-github-shenwei356-bio (= 0.0~git20200505.5afc28c-1), golang-github-shenwei356-bpool (= 0.0~git20160710.f9e0ee4-2), golang-github-shenwei356-breader (= 0.0~git20170924.21f0a70-2), golang-github-shenwei356-bwt (= 0.0~git20200418.ae79c98-2), golang-github-shenwei356-natsort (= 0.0~git20190418.600d539-2), golang-github-shenwei356-util (= 0.0~git20190523.f71ff37-2), golang-github-shenwei356-xopen (= 0.0~git20181203.f4f16dd-1), golang-github-spf13-cobra (= 0.0.7-1), golang-github-spf13-pflag (= 1.0.5-1), golang-github-tatsushid-go-prettytable (= 0.0~git20141013.ed2d14c-2), golang-go.crypto (= 1:0.0~git20200604.70a84ac-2), golang-golang-x-image (= 0.0~git20200119.58c2397-1), golang-golang-x-sys (= 0.0~git20200523.0598657-1), golang-gonum-v1-plot (= 0.7.0-1)
Section:science
Priority:optional
Homepage:https://github.com/shenwei356/seqkit
Description:
cross-platform and ultrafast toolkit for FASTA/Q file manipulation
 SeqKit describes a cross-platform ultrafast comprehensive toolkit for
 FASTA/Q processing. SeqKit provides executable binary files for all
 major operating systems, including Windows, Linux, and Mac OS X, and can
 be directly used without any dependencies or pre-configurations. SeqKit
 demonstrates competitive performance in execution time and memory usage
 compared to similar tools. The efficiency and usability of SeqKit enable
 researchers to rapidly accomplish common FASTA/Q file manipulations.
lintian 2.85.0~bpo10+1 check for seqkit_0.12.1+ds-1_amd64.deb (click to toggle)
E: seqkit: statically-linked-binary usr/lib/seqkit/benchmark
W: seqkit: hardening-no-pie usr/bin/seqkit
W: seqkit: hardening-no-relro usr/bin/seqkit
contents of seqkit_0.12.1+ds-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-08-03 16:19 ./
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/bin/
-rwxr-xr-x root/root  14961368 2020-08-03 16:19 ./usr/bin/seqkit
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/lib/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/lib/seqkit/
-rwxr-xr-x root/root   1602232 2020-08-03 16:19 ./usr/lib/seqkit/benchmark
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/doc/seqkit/
-rw-r--r-- root/root       160 2020-08-03 16:19 ./usr/share/doc/seqkit/changelog.Debian.gz
-rw-r--r-- root/root      8020 2020-04-21 14:36 ./usr/share/doc/seqkit/changelog.gz
-rw-r--r-- root/root      1435 2020-08-03 16:19 ./usr/share/doc/seqkit/copyright
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/man/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/man/man1/
-rw-r--r-- root/root       265 2020-08-03 16:19 ./usr/share/man/man1/seqkit-benchmark.1.gz
-rw-r--r-- root/root      1823 2020-08-03 16:19 ./usr/share/man/man1/seqkit.1.gz
lrwxrwxrwx root/root         0 2020-08-03 16:19 ./usr/bin/seqkit-benchmark -> ../lib/seqkit/benchmark
control file for seqkit-examples_0.12.1+ds-1_all.deb (click to toggle)
Package:seqkit-examples
Source:seqkit
Version:0.12.1+ds-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:35076
Section:science
Priority:optional
Homepage:https://github.com/shenwei356/seqkit
Description:
examples for seqkit: toolkit for FASTA/Q file manipulation
 SeqKit describes a cross-platform ultrafast comprehensive toolkit for
 FASTA/Q processing. SeqKit provides executable binary files for all
 major operating systems, including Windows, Linux, and Mac OS X, and can
 be directly used without any dependencies or pre-configurations. SeqKit
 demonstrates competitive performance in execution time and memory usage
 compared to similar tools. The efficiency and usability of SeqKit enable
 researchers to rapidly accomplish common FASTA/Q file manipulations.
 .
 This package contains a test data set as well as sample scripts
 running some test suite provided by Debian also as autopkgtest.
lintian 2.85.0~bpo10+1 check for seqkit-examples_0.12.1+ds-1_all.deb (click to toggle)
contents of seqkit-examples_0.12.1+ds-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-08-03 16:19 ./
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/
-rw-r--r-- root/root       160 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/changelog.Debian.gz
-rw-r--r-- root/root      8020 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/changelog.gz
-rw-r--r-- root/root      1435 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/copyright
-rw-r--r-- root/root   4756221 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/pcs109_5k.sam.gz
-rw-r--r-- root/root   4041245 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/pcs109_5k_prim.sam.gz
-rw-r--r-- root/root   4126244 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/pcs109_5k_spliced.sam.gz
-rw-r--r-- root/root       679 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/run-unit-test
drwxr-xr-x root/root         0 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/
-rw-r--r-- root/root       302 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/Illimina1.5.fq
-rw-r--r-- root/root    866675 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/Illimina1.8.fq.gz
-rw-r--r-- root/root       291 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/Lactococcus-lactis-phage-BK5-T-ORF25.fasta
-rw-r--r-- root/root     57770 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/SIRV_150601a.fasta.gz
-rw-r--r-- root/root         2 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/blank.fx
-rw-r--r-- root/root         1 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/blank1.fx
-rw-r--r-- root/root       154 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/contigs.fa
-rw-r--r-- root/root    225825 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/hairpin.fa.fai.gz
-rw-r--r-- root/root   1178657 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/hairpin.fa.gz
-rw-r--r-- root/root    414942 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/hairpin.fa.seqkit.fai.gz
-rw-r--r-- root/root       110 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/hsa.fa
-rw-r--r-- root/root    590878 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/mature.fa.gz
-rw-r--r-- root/root     57167 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/miRNA.diff.gz
-rw-r--r-- root/root      1306 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/mouse-p53-cds.fna
-rw-r--r-- root/root      1065 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/pcs109_5k.bam.bai.gz
-rw-r--r-- root/root   5246109 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/pcs109_5k.bam.gz
-rw-r--r-- root/root   4184448 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k.fq.gz
-rw-r--r-- root/root    202662 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_bam_NanoPlot.tsv.gz
-rw-r--r-- root/root    130008 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_bam_alignment_length.tsv.gz
-rw-r--r-- root/root    121827 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_bam_soft_clips_tab.tsv.gz
-rw-r--r-- root/root      1053 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_fish_regression.tsv
-rw-r--r-- root/root     30609 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_fq_NanoPlot.tsv.gz
-rw-r--r-- root/root      1050 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_prim.bam.bai.gz
-rw-r--r-- root/root   4365929 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_prim.bam.gz
-rw-r--r-- root/root    198662 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_prim_bam_NanoPplot.tsv.gz
-rw-r--r-- root/root       784 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_spliced.bam.bai
-rw-r--r-- root/root   4473080 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/pcs109_5k_spliced.bam.gz
-rw-r--r-- root/root    303319 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/reads_1.fq.gz
-rw-r--r-- root/root    276332 2020-08-03 16:19 ./usr/share/doc/seqkit-examples/tests/reads_2.fq.gz
-rw-r--r-- root/root      2405 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/sana_ground.fas.gz
-rw-r--r-- root/root      2332 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/sana_ground.fq.gz
-rw-r--r-- root/root      3024 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/scat_test.tsv.gz
-rw-r--r-- root/root      3878 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/test.sh.gz
-rw-r--r-- root/root      9570 2020-04-21 14:36 ./usr/share/doc/seqkit-examples/tests/titin.fas.gz

Timestamp: 04.08.2020 / 11:01:33 (UTC)