biology/consed: workbench for sequence assemblies biology/phred: base caller with quality evaluation biology/phrap: sequence assembler for shotgun sequencing Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs.
Created attachment 144093 [details] svn diff for biology/consed A files/patch-installConsed.perl D files/patch-scripts_addReads2Consed.perl D files/patch-scripts_determineReadTypes.perl A files/pkg-message.in A pkg-plist D pkg-plist.examples
Created attachment 144094 [details] svn diff for biology/phrap A pkg-plist
Created attachment 144095 [details] svn diff for biology/phred A files/pkg-message.in A pkg-plist
this should have been 3 separate PRs
The three distfiles are restricted in distribution. I'll try to get access and test the patches, then commit the updates.
Got contact with the restricted distfile administration, update seems possible. Waiting to receive the distfiles, then: Tests with those distfiles.
Got the ACK to get the academic license. Need to find license form, fill it out and submit it.
License agreement was sent to distsite, consed and phrap received, waiting for phred.
any news? Kurt, if you at least commit consed, you get mzaki's ports off this list: http://leaf.dragonflybsd.org/~marino/misc/screwed.maintained.txt
> Kurt, if you at least commit consed, you get mzaki's ports off this list: > http://leaf.dragonflybsd.org/~marino/misc/screwed.maintained.txt consed depends on phrab and phred, so we're in a bind here. I've poked the distsite again.
ah, right, I read the report backwards.
got phred, will test with all patches.
A commit references this bug: Author: pi Date: Sat Aug 23 18:05:03 UTC 2014 New revision: 365765 URL: http://svnweb.freebsd.org/changeset/ports/365765 Log: update ports: biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer) Changes: head/biology/consed/Makefile head/biology/consed/distinfo head/biology/consed/files/patch-installConsed.perl head/biology/consed/files/patch-scripts_addReads2Consed.perl head/biology/consed/files/patch-scripts_determineReadTypes.perl head/biology/consed/files/patch-scripts_phredPhrap head/biology/consed/files/pkg-message.in head/biology/consed/pkg-plist.examples head/biology/phrap/Makefile head/biology/phrap/distinfo head/biology/phrap/files/patch-alignments.c head/biology/phrap/files/patch-analyze_splices.c head/biology/phrap/files/patch-anomalies.c head/biology/phrap/files/patch-calf_utils.c head/biology/phrap/files/patch-call_subs.c head/biology/phrap/files/patch-cand_pairs.c head/biology/phrap/files/patch-contigs.c head/biology/phrap/files/patch-db.c head/biology/phrap/files/patch-makefile head/biology/phrap/files/patch-names.c head/biology/phrap/files/patch-nodes.c head/biology/phrap/files/patch-pairs.c head/biology/phrap/files/patch-qual.c head/biology/phrap/files/patch-readin.c head/biology/phrap/files/patch-segments.c head/biology/phrap/files/patch-tig_node.c head/biology/phrap/files/patch-weibull.c head/biology/phrap/files/patch-words.c head/biology/phrap/pkg-plist head/biology/phred/Makefile head/biology/phred/files/pkg-message.in
Thank you for the patches, committed finally!