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Bug 221165 - sci-biology/t-coffee-5.65: stabilization request
Summary: sci-biology/t-coffee-5.65: stabilization request
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: High normal (vote)
Assignee: Gentoo Science Biology related packages
URL:
Whiteboard:
Keywords: STABLEREQ
Depends on:
Blocks:
 
Reported: 2008-05-10 05:47 UTC by Martin Mokrejš
Modified: 2008-07-14 17:02 UTC (History)
1 user (show)

See Also:
Package list:
Runtime testing required: ---

Attachments
Resulting alignment - 1st possibility (sample_seq1.aln-1,687 bytes, text/plain)
2008-07-06 21:42 UTC, Olivier Fisette (RETIRED) 		Details
Resulting alignment - 2nd possibility (sample_seq1.aln-2,687 bytes, text/plain)
2008-07-06 21:42 UTC, Olivier Fisette (RETIRED) 		Details
View All Add an attachment (proposed patch, testcase, etc.)

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Description Martin Mokrejš 2008-05-10 05:47:51 UTC 
Please stabilize for x86 and amd64, on May 14 will be a month in the tree. ;-)
Comment 1 Olivier Fisette (RETIRED) gentoo-dev 2008-07-06 21:41:11 UTC 
Stable on amd64.

x86 and ppc:

To test, after compiling t-coffee, copy the "sample_seq1.fasta" file from "/usr/share/t-coffee/example" to your home directory. This file contains the amino acid sequences for four homologs of a protein in different species. Run "t_coffee sample_seq1.fasta" to have t-coffee align the sequences, calculate the alignment scores, construct a dendrogram, etc. Output files are created in the working directory.

You can check the validity of the calculations by comparing the file "sample_seq1.aln" with the files I am attaching. Both aligments are valid; you will (should) get one or the other depending on your CPU.
Comment 2 Olivier Fisette (RETIRED) gentoo-dev 2008-07-06 21:42:20 UTC 
Created attachment 159740 [details]
Resulting alignment - 1st possibility
Comment 3 Olivier Fisette (RETIRED) gentoo-dev 2008-07-06 21:42:45 UTC 
Created attachment 159741 [details]
Resulting alignment - 2nd possibility
Comment 4 Christian Faulhammer (RETIRED) gentoo-dev 2008-07-08 05:59:42 UTC 
x86 stable
Comment 5 nixnut (RETIRED) gentoo-dev 2008-07-14 17:02:44 UTC 
ppc stable. closing since we're last.