179327 2007-05-21 15:42 0000 sci-biology/t-coffee-4.96 stabilisation request 2007-07-01 14:51:32 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED CANTFIX P2 normal --- 1 ribosome@gentoo.org ribosome@gentoo.org ppc@gentoo.org ribosome@gentoo.org 2007-05-21 15:42:35 0000 I would appreciate if all supporting arches (x86, ppc) would stabilise sci-biology/t-coffee. It has been in Portage for a while and works well. Sources for the latest current stable version are no longer available, so I want to remove that version ASAP. Test instructions: 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 file I am attaching. (This output file is also available in the example directory, but it was created with an old version of the program, and the formatting is a bit different so you would have to compare the files manually. With the provided file, a diff should suffice.) The only difference between the files should be the CPU time used for the calculations. Thanks in advance, ribosome@gentoo.org 2007-05-21 17:32:48 0000 Created an attachment (id=119904) Reference sequence alignment fauli@gentoo.org 2007-05-22 07:49:56 0000 x86 stable nixnut@gentoo.org 2007-06-01 20:53:00 0000 I'm seeing some differences between the output of t-coffee and your file: diff sample_seq1.aln sample_seq1.aln.bugzie 1c1 < CLUSTAL FORMAT for T-COFFEE Version_4.96 [http://www.tcoffee.org], CPU=0.17 sec, SCORE=34, Nseq=4, Len=81 --- > CLUSTAL FORMAT for T-COFFEE Version_5.05 [http://www.tcoffee.org], CPU=0.08 sec, SCORE=33, Nseq=4, Len=81 2a3,4 > hmgl_trybr kkdsnapkramtsfmffssdfrskhsdls-----ivemskaagaawkelgpeerkvyeem > hmgt_mouse -----kpkrprsayniyvsesfqeakdds-----aqgklklvneawknlspeekqayiql 4d5 < hmgl_trybr kkdsnapkramtsfmffssdfrskhs-----dlsivemskaagaawkelgpeerkvyeem 6,7c7 < hmgt_mouse -----kpkrprsayniyvsesfqeakddsaqgkl-----klvneawknlspeekqayiql < ***. ::: .: .. .. . * . *: * : : --- > ***. ::: .: .. .. . . * . *: * : : 9d8 < hmgb_chite aatakqnyiralqeyern-gg 11d9 < hmgl_wheat anklkgeynkaiaaynkgesa 12a11,12 > hmgb_chite aatakqnyiralqeyern-gg > hmgl_wheat anklkgeynkaiaaynkgesa jakub@gentoo.org 2007-06-01 21:00:03 0000 beer >> coffee; sending back to maintainer... :P mabi@gentoo.org 2007-06-23 20:51:09 0000 confirmed on an another G4. ribosome? ribosome@gentoo.org 2007-06-29 15:38:40 0000 This should not happen, so I think it is best for version 4.96 not to be stabilised on PPC. These variations could be caused by the magnification of a small number-rounding difference. The differences are very small, though, and probably do not impact the alignment's validity, so I do not think it is necessary to mask t-coffee in the PPC profiles. This leaves the problem of missing sources for the last (and only) stable PPC version. I suggest dropping the stable keyword and having t-coffee available only in the testing branch (for PPC). What do you PPC folk think? pylon@gentoo.org 2007-07-01 14:51:32 0000 (In reply to comment #6) > This leaves the problem of missing sources for the last (and only) stable PPC > version. I suggest dropping the stable keyword and having t-coffee available > only in the testing branch (for PPC). > > What do you PPC folk think? That's okay for us. Just drop the stable-version and keep the current version ~ppc. So, let's close this bug. 119904 2007-05-21 17:32 0000 Reference sequence alignment sample_seq1.aln text/plain Q0xVU1RBTCBGT1JNQVQgZm9yIFQtQ09GRkVFIFZlcnNpb25fNS4wNSBbaHR0cDovL3d3dy50Y29m ZmVlLm9yZ10sIENQVT0wLjA4IHNlYywgU0NPUkU9MzMsIE5zZXE9NCwgTGVuPTgxIAoKaG1nbF90 cnliciAgICAgIGtrZHNuYXBrcmFtdHNmbWZmc3NkZnJza2hzZGxzLS0tLS1pdmVtc2thYWdhYXdr ZWxncGVlcmt2eWVlbQpobWd0X21vdXNlICAgICAgLS0tLS1rcGtycHJzYXluaXl2c2VzZnFlYWtk ZHMtLS0tLWFxZ2tsa2x2bmVhd2tubHNwZWVrcWF5aXFsCmhtZ2JfY2hpdGUgICAgICAtLS1hZGtw a3JwbHNheW1sd2xuc2FyZXNpa3JlbnBkZmstdnRldmFra2dnZWx3cmdsa2QtLWtzZXdlYWsKaG1n bF93aGVhdCAgICAgIC0tZHBua3BrcmFwc2FmZnZmbWdlZnJlZWZrcWtucGtua3N2YWF2Z2thYWdl cndrc2xzZXNla2FweXZhawogICAgICAgICAgICAgICAgICAgICAgKioqLiA6OjogLjogLi4gIC4u IC4gIC4gICAgICAgICAgKiAgLiAgKjogKiAgICA6ICA6ICAgCgpobWdsX3RyeWJyICAgICAgYWVr ZGtlcnlrcmVtLS0tLS0tLS0tCmhtZ3RfbW91c2UgICAgICBha2RkcmlyeWRuZW1rc3dlZXFtYWUK aG1nYl9jaGl0ZSAgICAgIGFhdGFrcW55aXJhbHFleWVybi1nZwpobWdsX3doZWF0ICAgICAgYW5r bGtnZXlua2FpYWF5bmtnZXNhCiAgICAgICAgICAgICAgICAqICAgOiAuKiAuIDogICAgICAgICAK CgoK