Bug 118548 - New port: biology/consed viewing and editing workbench for sequence assembly
New port: biology/consed viewing and editing workbench for sequence assembly
Status: Closed FIXED
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s)
Latest
Any Any
: Normal Affects Only Me
Assigned To: FreeBSD ports mailing list
:
Depends on:
Blocks:
  Show dependency treegraph
 
Reported: 2007-12-11 11:20 UTC by mzaki
Modified: 2008-05-24 08:10 UTC (History)
0 users

See Also:


Attachments
file.shar (88.49 KB, text/plain)
2007-12-11 11:20 UTC, mzaki
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Description mzaki 2007-12-11 11:20:01 UTC
Consed is a tool for viewing, editing, and finishing sequence assemblies.

The port is constituted of 4 parts:
  biology/phred: base caller with quality evaluation
  biology/phrap: sequence assembler for shotgun sequencing
  biology/consed: workbench
  biology/phd2fasta: small utility
All these can be used separately; however, most function of consed depends on the others.

Although these programs are licensed freely for academic and nonprofit purposes,
users have to contact the authors to get the softwares.
Phred (including phd2fasta) and phrap are emailed,
and consed can be downloaded to a restricted IP address.
For commercial users, the licensing fee is ca. $10,000 at the time of writing.

Fix: Patch attached with submission follows:
Comment 1 dfilter freebsd_committer 2008-05-24 08:00:41 UTC
edwin       2008-05-24 07:00:37 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/consed       Makefile distinfo pkg-descr 
                         pkg-plist.examples 
    biology/consed/files patch-misc_mktrace.c 
                         patch-scripts_addReads2Consed.perl 
                         patch-scripts_determineReadTypes.perl 
                         patch-scripts_phredPhrap 
  Log:
  New port: biology/consed viewing and editing workbench for sequence
  assembly
  
          Consed is a tool for viewing, editing, and finishing sequence assemblies.
  
          The port is constituted of 4 parts:
          biology/phred: base caller with quality evaluation
          biology/phrap: sequence assembler for shotgun sequencing
          biology/consed: workbench
          biology/phd2fasta: small utility
  
          All these can be used separately; however, most function
          of consed depends on the others.
  
          Although these programs are licensed freely for academic
          and nonprofit purposes, users have to contact the authors
          to get the softwares.
          Phred (including phd2fasta) and phrap are emailed,
          and consed can be downloaded to a restricted IP address.
          For commercial users, the licensing fee is ca. $10,000 at
          the time of writing.
  
  PR:             ports/118548
  Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  
  Revision  Changes    Path
  1.98      +1 -0      ports/biology/Makefile
  1.1       +104 -0    ports/biology/consed/Makefile (new)
  1.1       +3 -0      ports/biology/consed/distinfo (new)
  1.1       +14 -0     ports/biology/consed/files/patch-misc_mktrace.c (new)
  1.1       +11 -0     ports/biology/consed/files/patch-scripts_addReads2Consed.perl (new)
  1.1       +11 -0     ports/biology/consed/files/patch-scripts_determineReadTypes.perl (new)
  1.1       +36 -0     ports/biology/consed/files/patch-scripts_phredPhrap (new)
  1.1       +4 -0      ports/biology/consed/pkg-descr (new)
  1.1       +990 -0    ports/biology/consed/pkg-plist.examples (new)
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Comment 2 dfilter freebsd_committer 2008-05-24 08:01:59 UTC
edwin       2008-05-24 07:01:56 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/phd2fasta    Makefile distinfo pkg-descr 
    biology/phd2fasta/files patch-Makefile 
  Log:
  New port: biology/consed viewing and editing workbench for sequence
  assembly
  
          Consed is a tool for viewing, editing, and finishing sequence
          assemblies.
  
          The port is constituted of 4 parts:
          biology/phred: base caller with quality evaluation
          biology/phrap: sequence assembler for shotgun sequencing
          biology/consed: workbench
          biology/phd2fasta: small utility
  
          All these can be used separately; however, most function
          of consed depends on the others.
  
          Although these programs are licensed freely for academic
          and nonprofit purposes, users have to contact the authors
          to get the softwares.
          Phred (including phd2fasta) and phrap are emailed,
          and consed can be downloaded to a restricted IP address.
          For commercial users, the licensing fee is ca. $10,000 at
          the time of writing.
  
  PR:             ports/118548
  Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  
  Revision  Changes    Path
  1.99      +1 -0      ports/biology/Makefile
  1.1       +48 -0     ports/biology/phd2fasta/Makefile (new)
  1.1       +3 -0      ports/biology/phd2fasta/distinfo (new)
  1.1       +10 -0     ports/biology/phd2fasta/files/patch-Makefile (new)
  1.1       +8 -0      ports/biology/phd2fasta/pkg-descr (new)
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Comment 3 Edwin Groothuis freebsd_committer 2008-05-24 08:03:25 UTC
State Changed
From-To: open->closed

Committed, thanks!
Comment 4 dfilter freebsd_committer 2008-05-24 08:03:28 UTC
edwin       2008-05-24 07:03:23 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/phrap        Makefile distinfo pkg-descr 
    biology/phrap/files  patch-makefile 
  Log:
  New port: biology/consed viewing and editing workbench for sequence
  assembly
  
          Consed is a tool for viewing, editing, and finishing sequence
          assemblies.
  
          The port is constituted of 4 parts:
          biology/phred: base caller with quality evaluation
          biology/phrap: sequence assembler for shotgun sequencing
          biology/consed: workbench
          biology/phd2fasta: small utility
  
          All these can be used separately; however, most function
          of consed depends on the others.
  
          Although these programs are licensed freely for academic
          and nonprofit purposes, users have to contact the authors
          to get the softwares.
          Phred (including phd2fasta) and phrap are emailed,
          and consed can be downloaded to a restricted IP address.
          For commercial users, the licensing fee is ca. $10,000 at
          the time of writing.
  
  PR:             ports/118548
  Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  
  Revision  Changes    Path
  1.100     +1 -0      ports/biology/Makefile
  1.1       +62 -0     ports/biology/phrap/Makefile (new)
  1.1       +3 -0      ports/biology/phrap/distinfo (new)
  1.1       +27 -0     ports/biology/phrap/files/patch-makefile (new)
  1.1       +21 -0     ports/biology/phrap/pkg-descr (new)
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Comment 5 dfilter freebsd_committer 2008-05-24 08:04:55 UTC
edwin       2008-05-24 07:04:45 UTC

  FreeBSD ports repository

  Modified files:
    biology              Makefile 
  Added files:
    biology/phred        Makefile distinfo pkg-descr 
    biology/phred/files  patch-Makefile 
  Log:
  New port: biology/consed viewing and editing workbench for sequence
  assembly
  
          Consed is a tool for viewing, editing, and finishing sequence
          assemblies.
  
          The port is constituted of 4 parts:
          biology/phred: base caller with quality evaluation
          biology/phrap: sequence assembler for shotgun sequencing
          biology/consed: workbench
          biology/phd2fasta: small utility
  
          All these can be used separately; however, most function
          of consed depends on the others.
  
          Although these programs are licensed freely for academic
          and nonprofit purposes, users have to contact the authors
          to get the softwares.
          Phred (including phd2fasta) and phrap are emailed,
          and consed can be downloaded to a restricted IP address.
          For commercial users, the licensing fee is ca. $10,000 at
          the time of writing.
  
  PR:             ports/118548
  Submitted by:   Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  
  Revision  Changes    Path
  1.101     +1 -0      ports/biology/Makefile
  1.1       +67 -0     ports/biology/phred/Makefile (new)
  1.1       +3 -0      ports/biology/phred/distinfo (new)
  1.1       +13 -0     ports/biology/phred/files/patch-Makefile (new)
  1.1       +24 -0     ports/biology/phred/pkg-descr (new)
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To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"