112769 2005-11-16 19:36 0000 Added MPI support for sci-biology/clustalw 2005-11-19 15:18:01 0000 1 1 1 Unclassified Gentoo Linux Ebuilds unspecified All Linux RESOLVED FIXED P2 enhancement --- 1 gentoo@gecka.us sci@gentoo.org gentoo@gecka.us 2005-11-16 19:36:13 0000 A build to add MPI support to ClustalW. It is stand alone program so no modification of the clustalw ebuild is needed. gentoo@gecka.us 2005-11-16 19:38:26 0000 Created an attachment (id=73051) The ebuild I made. This is the Ebuild I made. It needs platform support, directory clean up and such all finalized. I am not an expert ebuild writer so I am sure there is much better ways to do some of this. ribosome@gentoo.org 2005-11-19 09:30:06 0000 Thanks for your work, Brady. This is now in Portage as a new package called "sci-biology/clustalw-mpi". (I decided to use a new package rather than add the "mpi" USE flag to "clustalw" because this is a stand-alone alternative implementation and not just a patch for the original program.) I modified your ebuild to honor the user's USE flags, and added USE flags to control some options of the build process (MPI code for NJ trees, static scheduling for pair alignments). ribosome@gentoo.org 2005-11-19 09:39:46 0000 (In reply to comment #2) > I modified your ebuild to honor the user's USE flags, I meant to say CFLAGS. gentoo@gecka.us 2005-11-19 15:18:01 0000 Wow! cool thanks =) I have a bucket more custom ebuilds for programs we use here. Let me know if you want me to upload any of them. My list includes: sci-biology: fluctuate, lamarc, modeltest, phrap, s3, xplor-nih, fastDNAml, genetree, migrate, paml, repeatmasker, seq-gen sci-mathematics: rproject sci-misc: oommf Soemthing like 1/3 of those have fetch restrictions because they can not be downloaded without first contacting the authors (for grant reasons..) 73051 2005-11-16 19:38 0000 The ebuild I made. clustalw-mpi-0.13.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA1IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgoKaW5oZXJp dCB0b29sY2hhaW4tZnVuY3MKCkRFU0NSSVBUSU9OPSJHZW5lcmFsIHB1cnBvc2UgbXVsdGlwbGUg YWxpZ25tZW50IHByb2dyYW0gZm9yIEROQSBhbmQgcHJvdGVpbnMiCkhPTUVQQUdFPSJodHRwOi8v d2ViLmJpaS5hLXN0YXIuZWR1LnNnL35rdW9iaW4vY2x1c3RhbHctbXBpLyIKU1JDX1VSST0iaHR0 cDovL3dlYi5iaWkuYS1zdGFyLmVkdS5zZy9+a3VvYmluL2NsdXN0YWx3LW1waS9jbHVzdGFsdy1t cGktJHtQVn0udGFyLmd6IgoKTElDRU5TRT0iY2x1c3RhbHciClNMT1Q9IjAiCktFWVdPUkRTPSJh bHBoYSBhbWQ2NCBwcGMgcHBjLW1hY29zIHBwYzY0IHNwYXJjIHg4NiIKSVVTRT0iIgoKREVQRU5E PSJ2aXJ0dWFsL2xpYmMKICAgICAgICB2aXJ0dWFsL21waSAiCgpTPSR7V09SS0RJUn0vJHtQTn0t JHtQVn0KCnNyY19jb21waWxlKCkgewoJZW1ha2UgfHwgZGllCn0KCnNyY19pbnN0YWxsKCkgewoJ ZG9iaW4gY2x1c3RhbHctbXBpIHx8IGRpZQp9Cg==