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fasta3_36.3.8h.2020-02-11-1_amd64.changes (click to toggle)
Format:1.8
Date:Tue, 11 Feb 2020 18:30:49 +0100
Source:fasta3
Binary:fasta3 fasta3-dbgsym fasta3-doc
Architecture:source amd64 all
Version:36.3.8h.2020-02-11-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Andreas Tille <tille@debian.org>
Description:
fasta3     - tools for searching collections of biological sequences
fasta3-doc - user guide for FASTA tools
Changes:
fasta3 (36.3.8h.2020-02-11-1) unstable; urgency=medium

  * Team upload
  * New upstream version with free license
    Licenses was changed from Academics-only to BSD-2-clause
  * Point watch file to Github
  * Standards-Version: 4.5.0 (routine-update)
  * Set upstream metadata fields: Bug-Database, Bug-Submit.
Files:
1237a13b72005f2859d3d7ca8a4eec75 2076 science optional fasta3_36.3.8h.2020-02-11-1.dsc
32be68d48f54aee1d6c45ef4cc2dcc59 1257160 science optional fasta3_36.3.8h.2020-02-11.orig.tar.gz
90fb896fa687810fd96548b39f88ca22 5420 science optional fasta3_36.3.8h.2020-02-11-1.debian.tar.xz
a9ed9af5c700bc3a905a0fd7e9a3ef83 3092940 debug optional fasta3-dbgsym_36.3.8h.2020-02-11-1_amd64.deb
8cffe36538da21fae93dd018f6b47590 271180 doc optional fasta3-doc_36.3.8h.2020-02-11-1_all.deb
b18f205359d5c4300a202a4389a06ad0 6230 science optional fasta3_36.3.8h.2020-02-11-1_amd64.buildinfo
cfa727f9836edf343c73532801f51eb7 460708 science optional fasta3_36.3.8h.2020-02-11-1_amd64.deb
fasta3_36.3.8h.2020-02-11-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:fasta3
Binary:fasta3, fasta3-doc
Architecture:any all
Version:36.3.8h.2020-02-11-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Steffen Moeller <moeller@debian.org>
Homepage:https://fasta.bioch.virginia.edu
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/fasta3
Vcs-Git:https://salsa.debian.org/med-team/fasta3.git
Build-Depends:debhelper-compat (=12), zlib1g-dev
Package-List:fasta3 deb science optional arch=any fasta3-doc deb doc optional arch=all
Files:
32be68d48f54aee1d6c45ef4cc2dcc59 1257160 fasta3_36.3.8h.2020-02-11.orig.tar.gz
90fb896fa687810fd96548b39f88ca22 5420 fasta3_36.3.8h.2020-02-11-1.debian.tar.xz
lintian 2.49.0~bpo9+1 check for fasta3_36.3.8h.2020-02-11-1.dsc (click to toggle)
README.source for fasta3_36.3.8h.2020-02-11-1.dsc (click to toggle)
The source code could be freed in principle.  See

    https://lists.debian.org/debian-med/2019/09/msg00039.html

Unfortunately the explicitly free code that is in the archive

    http://eddylab.org/software/swsse2/swsse2.tar.gz

is older than the files here and thus we can not just package
the freely licensed code and replace the one in fasta3.

 -- Andreas Tille <tille@debian.org>  Sat, 08 Feb 2020 19:30:24 +0100

control file for fasta3_36.3.8h.2020-02-11-1_amd64.deb (click to toggle)
Package:fasta3
Version:36.3.8h.2020-02-11-1
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:5254
Depends:libc6 (>=2.29)
Section:science
Priority:optional
Homepage:https://fasta.bioch.virginia.edu
Description:
tools for searching collections of biological sequences
 The FASTA programs find regions of local or global similarity between
 Protein or DNA sequences, either by searching Protein or DNA databases,
 or by identifying local duplications within a sequence. Other
 programs provide information on the statistical significance of an
 alignment. Like BLAST, FASTA can be used to infer functional and
 evolutionary relationships between sequences as well as help identify
 members of gene families.
 .
  * Protein
    - Protein-protein FASTA
    - Protein-protein Smith-Waterman (ssearch)
    - Global Protein-protein (Needleman-Wunsch) (ggsearch)
    - Global/Local protein-protein (glsearch)
    - Protein-protein with unordered peptides (fasts)
    - Protein-protein with mixed peptide sequences (fastf)
 .
  * Nucleotide
    - Nucleotide-Nucleotide (DNA/RNA fasta)
    - Ordered Nucleotides vs Nucleotide (fastm)
    - Un-ordered Nucleotides vs Nucleotide (fasts)
 .
  * Translated
    - Translated DNA (with frameshifts, e.g. ESTs)
      vs Proteins (fastx/fasty)
    - Protein vs Translated DNA (with frameshifts)
      (tfastx/tfasty)
    - Peptides vs Translated DNA (tfasts)
 .
  * Statistical Significance
    - Protein vs Protein shuffle (prss)
    - DNA vs DNA shuffle (prss)
    - Translated DNA vs Protein shuffle (prfx)
 .
  * Local Duplications
    - Local Protein alignments (lalign)
    - Plot Protein alignment "dot-plot" (plalign)
    - Local DNA alignments (lalign)
    - Plot DNA alignment "dot-plot" (plalign)
 .
 This software is often used via a web service at the
 EBI with readily indexed reference databases at
 http://www.ebi.ac.uk/Tools/fasta/.
lintian 2.49.0~bpo9+1 check for fasta3_36.3.8h.2020-02-11-1_amd64.deb (click to toggle)
W: fasta3: binary-without-manpage usr/bin/fastf36
W: fasta3: binary-without-manpage usr/bin/fastm36
W: fasta3: binary-without-manpage usr/bin/fasts36
W: fasta3: binary-without-manpage usr/bin/fastx36
W: fasta3: binary-without-manpage usr/bin/fasty36
W: fasta3: binary-without-manpage usr/bin/ggsearch36
W: fasta3: binary-without-manpage usr/bin/glsearch36
W: fasta3: binary-without-manpage usr/bin/lalign36
W: fasta3: binary-without-manpage usr/bin/ssearch36
W: fasta3: binary-without-manpage usr/bin/tfastf36
W: fasta3: binary-without-manpage usr/bin/tfastm36
W: fasta3: binary-without-manpage usr/bin/tfasts36
W: fasta3: binary-without-manpage usr/bin/tfastx36
W: fasta3: binary-without-manpage usr/bin/tfasty36
W: fasta3: manpage-has-bad-whatis-entry usr/share/man/man1/ps_lav.1.gz
W: fasta3: manpage-has-errors-from-man usr/share/man/man1/fastf3.1.gz 35: warning: macro `Y',' not defined
W: fasta3: manpage-has-errors-from-man usr/share/man/man1/prss3.1.gz 54: warning: macro `z-values'' not defined
W: fasta3: manpage-section-mismatch usr/share/man/man1/map_db.1.gz:1 1 != September, 1999
contents of fasta3_36.3.8h.2020-02-11-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-02-11 17:30 ./
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/bin/
-rwxr-xr-x root/root    369784 2020-02-11 17:30 ./usr/bin/fasta36
-rwxr-xr-x root/root    325720 2020-02-11 17:30 ./usr/bin/fastf36
-rwxr-xr-x root/root    329752 2020-02-11 17:30 ./usr/bin/fastm36
-rwxr-xr-x root/root    329752 2020-02-11 17:30 ./usr/bin/fasts36
-rwxr-xr-x root/root    365944 2020-02-11 17:30 ./usr/bin/fastx36
-rwxr-xr-x root/root    365944 2020-02-11 17:30 ./usr/bin/fasty36
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-rwxr-xr-x root/root    377864 2020-02-11 17:30 ./usr/bin/glsearch36
-rwxr-xr-x root/root    369640 2020-02-11 17:30 ./usr/bin/lalign36
-rwxr-xr-x root/root     18920 2020-02-11 17:30 ./usr/bin/map_db
-rwxr-xr-x root/root    373928 2020-02-11 17:30 ./usr/bin/ssearch36
-rwxr-xr-x root/root    330200 2020-02-11 17:30 ./usr/bin/tfastf36
-rwxr-xr-x root/root    334232 2020-02-11 17:30 ./usr/bin/tfastm36
-rwxr-xr-x root/root    334232 2020-02-11 17:30 ./usr/bin/tfasts36
-rwxr-xr-x root/root    365944 2020-02-11 17:30 ./usr/bin/tfastx36
-rwxr-xr-x root/root    365944 2020-02-11 17:30 ./usr/bin/tfasty36
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc/fasta3/
-rw-r--r-- root/root       858 2020-02-11 17:30 ./usr/share/doc/fasta3/changelog.Debian.gz
-rw-r--r-- root/root      2874 2020-02-11 17:30 ./usr/share/doc/fasta3/copyright
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/man/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/man/man1/
-rw-r--r-- root/root      7358 2020-02-11 17:30 ./usr/share/man/man1/fasta36.1.gz
-rw-r--r-- root/root      2195 2020-02-11 17:30 ./usr/share/man/man1/fastf3.1.gz
-rw-r--r-- root/root      2119 2020-02-11 17:30 ./usr/share/man/man1/fasts3.1.gz
-rw-r--r-- root/root       523 2020-02-11 17:30 ./usr/share/man/man1/map_db.1.gz
-rw-r--r-- root/root      2146 2020-02-11 17:30 ./usr/share/man/man1/prss3.1.gz
-rw-r--r-- root/root       402 2020-02-11 17:30 ./usr/share/man/man1/ps_lav.1.gz
control file for fasta3-dbgsym_36.3.8h.2020-02-11-1_amd64.deb (click to toggle)
Package:fasta3-dbgsym
Source:fasta3
Version:36.3.8h.2020-02-11-1
Auto-Built-Package:debug-symbols
Architecture:amd64
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:4050
Depends:fasta3 (=36.3.8h.2020-02-11-1)
Section:debug
Priority:optional
Description:
debug symbols for fasta3
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lintian 2.49.0~bpo9+1 check for fasta3-dbgsym_36.3.8h.2020-02-11-1_amd64.deb (click to toggle)
contents of fasta3-dbgsym_36.3.8h.2020-02-11-1_amd64.deb (click to toggle)
drwxr-xr-x root/root         0 2020-02-11 17:30 ./
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/lib/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/lib/debug/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/lib/debug/.build-id/
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-rw-r--r-- root/root    293128 2020-02-11 17:30 ./usr/lib/debug/.build-id/fd/ec07cac54ec39f9c291cfc4d6f5d75334020af.debug
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/lib/debug/.dwz/x86_64-linux-gnu/
-rw-r--r-- root/root     32672 2020-02-11 17:30 ./usr/lib/debug/.dwz/x86_64-linux-gnu/fasta3.debug
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc/
lrwxrwxrwx root/root         0 2020-02-11 17:30 ./usr/share/doc/fasta3-dbgsym -> fasta3
control file for fasta3-doc_36.3.8h.2020-02-11-1_all.deb (click to toggle)
Package:fasta3-doc
Source:fasta3
Version:36.3.8h.2020-02-11-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:276
Breaks:fasta3 (<< 36.3.8h)
Replaces:fasta3 (<< 36.3.8h)
Section:doc
Priority:optional
Homepage:https://fasta.bioch.virginia.edu
Description:
user guide for FASTA tools
 The FASTA programs find regions of local or global similarity between
 Protein or DNA sequences, either by searching Protein or DNA databases,
 or by identifying local duplications within a sequence. Other
 programs provide information on the statistical significance of an
 alignment. Like BLAST, FASTA can be used to infer functional and
 evolutionary relationships between sequences as well as help identify
 members of gene families.
 .
 The use of the package's many binaries and the equally representated
 conceptual approaches towards sequence analyses are summarised in
 this PDF.
lintian 2.49.0~bpo9+1 check for fasta3-doc_36.3.8h.2020-02-11-1_all.deb (click to toggle)
contents of fasta3-doc_36.3.8h.2020-02-11-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-02-11 17:30 ./
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc/fasta3/
-rw-r--r-- root/root    268476 2020-02-10 19:14 ./usr/share/doc/fasta3/fasta_guide.pdf
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc/fasta3-doc/
-rw-r--r-- root/root       858 2020-02-11 17:30 ./usr/share/doc/fasta3-doc/changelog.Debian.gz
-rw-r--r-- root/root      2874 2020-02-11 17:30 ./usr/share/doc/fasta3-doc/copyright
drwxr-xr-x root/root         0 2020-02-11 17:30 ./usr/share/doc-base/
-rw-r--r-- root/root       678 2020-02-11 17:30 ./usr/share/doc-base/fasta3

Timestamp: 11.02.2020 / 18:01:29 (UTC)