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:
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) _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
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) _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
State Changed From-To: open->closed Committed, thanks!
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) _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
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) _______________________________________________ cvs-all@freebsd.org mailing list http://lists.freebsd.org/mailman/listinfo/cvs-all To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"