Bug 206900 - [NEW PORT] biology/samtools0119: Generic format for storing large nucleotide sequence alignments
Summary: [NEW PORT] biology/samtools0119: Generic format for storing large nucleotide ...
Status: Closed Overcome By Events
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: --- Affects Some People
Assignee: Kubilay Kocak
URL:
Keywords: feature, patch
Depends on:
Blocks:
 
Reported: 2016-02-03 19:22 UTC by Jason W. Bacon
Modified: 2016-02-26 04:08 UTC (History)
1 user (show)

See Also:

Attachments
Poudriere log (27.86 KB, text/plain)
2016-02-03 19:22 UTC, Jason W. Bacon 		no flags Details
Poudriere log (26.59 KB, text/plain)
2016-02-03 19:23 UTC, Jason W. Bacon 		no flags Details
Poudriere log (29.83 KB, text/plain)
2016-02-03 19:24 UTC, Jason W. Bacon 		no flags Details
Poudriere log (32.44 KB, text/plain)
2016-02-03 19:24 UTC, Jason W. Bacon 		no flags Details
Shar archive (4.81 KB, text/plain)
2016-02-04 13:39 UTC, Jason W. Bacon 		no flags Details
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Description Jason W. Bacon freebsd_committer freebsd_triage 2016-02-03 19:22:58 UTC 
Created attachment 166521 [details]
Poudriere log

SAM (Sequence Alignment/Map) format is a generic format for storing large
nucleotide sequence alignments.

This port provides support for some genomics tools such as Trinity and dDocent which do not work with samtools 1.x.
Comment 1 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-03 19:23:36 UTC 
Created attachment 166522 [details]
Poudriere log
Comment 2 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-03 19:24:09 UTC 
Created attachment 166523 [details]
Poudriere log
Comment 3 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-03 19:24:37 UTC 
Created attachment 166524 [details]
Poudriere log
Comment 4 Kubilay Kocak freebsd_committer freebsd_triage 2016-02-04 06:55:50 UTC 
@Jason,

Is there supposed to be a shell archive (shar) attached?

Also, there's no need to set approval for logs (as they are logs, and dont need approval, only changes/patches)
Comment 5 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-04 13:39:51 UTC 
Created attachment 166559 [details]
Shar archive


Oh, jeez...  Shar is attached.
Comment 6 John Marino freebsd_committer freebsd_triage 2016-02-05 08:15:47 UTC 
there is already a biology/samstools and I don't see that mentioned anywhere, nor how 0119 related to it, nor why there needs to be two ports of the same thing.
Comment 7 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-05 13:26:27 UTC 
That's explained in the comment submitted with the PR.  There are some genomics tools that don't work with samtools 1.x.  We've tried it.  We either get poor performance or the pipeline breaks down entirely.
Comment 8 John Marino freebsd_committer freebsd_triage 2016-02-05 13:29:25 UTC 
I missed it.
But is this a fork?  if it's just a newer version of samstool, it should replace the current version, right?

so I'll ask again: Are both versions needed?  Or can this one here do everything?
Comment 9 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-05 13:38:45 UTC 
This is an *older* version, 0.1.19 vs 1.3.  (The last releases before 1.0)  I  hope we can eliminate it eventually and just use the latest stable for everything, but from what I've experienced porting genomics tools, that could take a couple years.
Comment 10 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-08 22:41:53 UTC 
Coincidentally, there seems to finally be some movement in tools that depend on samtools.  The rsem project just released a new version compatible with samtools 1.3.  I'll attempt a Trinity build using samtools 1.3 and if I succeed, will benchmark it for comparison with the samtools 0.1.19 build.  Hold off on this PR until I report back.
Comment 11 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-09 00:09:21 UTC 
Trinity and rsem appear to be working with a slightly modified samtools 1.3.  ( See 207032 )

For now, I'd like to focus on getting Trinity committed.  The other ports that depend on samtools 0.1.19 can wait.

The following PRs + more to come will be required by Trinity:

206926
206939
207032

Thanks,

    Jason
Comment 12 Jason W. Bacon freebsd_committer freebsd_triage 2016-02-26 03:23:37 UTC 
Please close this PR.  I've found a way to work with the existing samtools port for our short-term needs.