diff options
37 files changed, 139 insertions, 189 deletions
diff --git a/sci-biology/align_to_scf/Manifest b/sci-biology/align_to_scf/Manifest index 1989dbb9e..ef3f6767e 100644 --- a/sci-biology/align_to_scf/Manifest +++ b/sci-biology/align_to_scf/Manifest @@ -1,3 +1,4 @@ +AUX README 1416 RMD160 72720412dea59c15598b4283ce35122689631052 SHA1 43116fb64f89c44edc47b624245f781e76ebb2b9 SHA256 37cd52c0578437e1a00a107049e4c410728ab09b2e778313c47e3a74f335fb2d DIST align_to_scf-1.06.tgz 25463 RMD160 1881affac69053fbc4677474451eed4a1d2c30f3 SHA1 6ec49824d30d1e892b257aba11d03f943c15663a SHA256 792d5023d02570cfb8510adb102ddacc3795ef5689e91c96e9e56b304ec70ddb -EBUILD align_to_scf-1.06.ebuild 674 RMD160 adc9b5a8d1eee62bdd07434dc15de1d049e237a3 SHA1 3b0cd0afb67f3f971fee24738c6927b432a0116b SHA256 17fad3e50dd0276433b9c060358410d70087b90928aec38701c5af866db9483f -MISC metadata.xml 261 RMD160 ce19afc5fdd536a9eadb35a705f09613e3774e32 SHA1 b95b491e808c8dd5a106edae7e48af4f8d61f58a SHA256 e3766426d46af16432093cd9fb8a2df3862c77ef313ad175ca2ef60af5cee6f5 +EBUILD align_to_scf-1.06.ebuild 761 RMD160 1cfe95a673c7dfacd4c438350dce531bbc295df1 SHA1 f530cd0209ed7def26d75297ab58d07276496960 SHA256 415c0c2e0fc46efc1a361f6ca8d62fdc2295f09142b1e1ec59463643e239508f +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/sci-biology/align_to_scf/align_to_scf-1.06.ebuild b/sci-biology/align_to_scf/align_to_scf-1.06.ebuild index fa507fbca..cb6cc7815 100644 --- a/sci-biology/align_to_scf/align_to_scf-1.06.ebuild +++ b/sci-biology/align_to_scf/align_to_scf-1.06.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -DESCRIPTION="This is used by sci-biology/roche454ace2caf.pl" +DESCRIPTION="Provide data to staden to view trace information at a given position missing from Roche .ace files" HOMEPAGE="http://genome.imb-jena.de/software/roche454ace2caf" SRC_URI="http://genome.imb-jena.de/software/roche454ace2caf/download/src/align_to_scf-1.06.tgz" @@ -25,4 +25,5 @@ src_prepare(){ src_install(){ dobin align_to_scf || die + dodoc "${FILESDIR}"/README || die } diff --git a/sci-biology/align_to_scf/files/README b/sci-biology/align_to_scf/files/README new file mode 100644 index 000000000..be51f6fdd --- /dev/null +++ b/sci-biology/align_to_scf/files/README @@ -0,0 +1,37 @@ +* What's about "align_to_scf" ? + + This is important if you want to see the real traces within the contig editor from STADEN at a given position. + + Note: there are no information given within the ACE assembly to recalculate the trace position backward from assembly. + STADEN "trev" will access/open traces as given from "sequencer machine" and Roche assembly give you only the complete assembly + information. This is the problem ! + + Are you firm with gap4 ? + The program "trev" is automatically called within "gap4". + And you start this with: + -> open gap4 database + --> open contig editor, select contig + ---> double-click on one letter will open this trace at this position and set cursor to exact this position ! + double-click on the consensus line will open all traces at this position ! + + You can also see the "slack" by enable/disable "show cutoff"; + + Example ? + Try this very simple test data and verify this letter by letter: + + + % align_to_scf -f test.qry -o test.aln + + --- test.qry --- + >F0FH8BE01EUM6Y <- name of read from sff archive + ATGCATCATG-ATGC <- fasta sequence of this read from ace file + ATGCATGCATGCATGC <- fasta sequence of this read from sff trace file + + + And you should get this output "test.aln" ( see also CAF format description ) : + + >F0FH8BE01EUM6Y + Align_to_SCF 1 6 1 6 + Align_to_SCF 7 10 8 11 + Align_to_SCF 12 15 13 16 + diff --git a/sci-biology/align_to_scf/metadata.xml b/sci-biology/align_to_scf/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/align_to_scf/metadata.xml +++ b/sci-biology/align_to_scf/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml index 663ee326d..b6e8ca8b0 100644 --- a/sci-biology/amos/metadata.xml +++ b/sci-biology/amos/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>AMOS is collection of tools and class interfaces for the assembly of DNA sequencing reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation</longdescription> diff --git a/sci-biology/apollo/metadata.xml b/sci-biology/apollo/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/apollo/metadata.xml +++ b/sci-biology/apollo/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/argo-bin/metadata.xml b/sci-biology/argo-bin/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/argo-bin/metadata.xml +++ b/sci-biology/argo-bin/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/argo/metadata.xml b/sci-biology/argo/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/argo/metadata.xml +++ b/sci-biology/argo/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/autoeditor/metadata.xml b/sci-biology/autoeditor/metadata.xml index 7b9b5a9a0..5990f62d7 100644 --- a/sci-biology/autoeditor/metadata.xml +++ b/sci-biology/autoeditor/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>AutoEditor is a program that can automatically correct discrepancies in a diff --git a/sci-biology/bambus/metadata.xml b/sci-biology/bambus/metadata.xml index 5b7de1033..8d87f01b2 100644 --- a/sci-biology/bambus/metadata.xml +++ b/sci-biology/bambus/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>Bambus is the first general purpose scaffolder that is publicly available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.</longdescription> diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index 2ab82ccb0..e10e62143 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index 28aad7623..7789d7d4f 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>no-herd</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>BEDTools: a flexible suite of utilities for comparing genomic features.</longdescription> diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml index fe1df42bc..4f255d9b2 100644 --- a/sci-biology/caftools/metadata.xml +++ b/sci-biology/caftools/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data.</longdescription> diff --git a/sci-biology/cap3-bin/metadata.xml b/sci-biology/cap3-bin/metadata.xml index 3bfd53b03..3cc8fb68b 100644 --- a/sci-biology/cap3-bin/metadata.xml +++ b/sci-biology/cap3-bin/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>CAP3 is an EST (Expressed Sequence Tag) assembler, coping with alternatively spliced variants</longdescription> diff --git a/sci-biology/cdbfasta/metadata.xml b/sci-biology/cdbfasta/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/cdbfasta/metadata.xml +++ b/sci-biology/cdbfasta/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/clview/metadata.xml +++ b/sci-biology/clview/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/nrcl/metadata.xml b/sci-biology/nrcl/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/nrcl/metadata.xml +++ b/sci-biology/nrcl/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/psx/metadata.xml b/sci-biology/psx/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/psx/metadata.xml +++ b/sci-biology/psx/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-biology/roche454ace2caf/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/roche454ace2caf/metadata.xml +++ b/sci-biology/roche454ace2caf/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/sclust/metadata.xml b/sci-biology/sclust/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/sclust/metadata.xml +++ b/sci-biology/sclust/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/seqclean/metadata.xml b/sci-biology/seqclean/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/seqclean/metadata.xml +++ b/sci-biology/seqclean/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/sff_dump/metadata.xml b/sci-biology/sff_dump/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/sff_dump/metadata.xml +++ b/sci-biology/sff_dump/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/staden/metadata.xml +++ b/sci-biology/staden/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index 8bb2fc343..54cc2530a 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,3 +1,5 @@ +AUX response.varfile 257 RMD160 f78b619ca82de34535f5834fcc78fa549b064a71 SHA1 369b0eab764fbdfe73cc5473471a855d21a711d7 SHA256 547580fbc96ea0c42ae8832e2ffa5cfbab8ac1a77d2129e08e901b36f42f4c45 DIST coveragestats.py 4800 RMD160 a45ef0ef293d08c62f79d4921c810554cea5cc44 SHA1 87b2e3432919c8cd2eb673bd8cf4a59f34d4a58e SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc DIST tablet_linux_x86_1_10_09_20.sh 23501634 RMD160 74e5f4c647aa105d4a51602059e593fe2595eeae SHA1 71b1a2aaf42bac49671c0b517f041b7c2254ce41 SHA256 2d8b86fe0e88aa1bbc5d2916a09d7f3b0df339069024191a07fbd83cf73dec41 -EBUILD tablet-bin-1.10.09.20.ebuild 1286 RMD160 98074cbf33fb5c4bf87fea8cfdd8a0d489a226b1 SHA1 dcfaa500169b9389fa40741522ac1f9f1b6b7d87 SHA256 e56e7f94b315ef499cf42cbaa667d8c91a6f30954982f9bb8cb1217d43f3bdb9 +EBUILD tablet-bin-1.10.09.20.ebuild 1464 RMD160 016c74d519d4c1e2775985a922f6856a483b4fb6 SHA1 7222f8d09dee8051bb4da96ed76e065e9da6bc2a SHA256 7d8453ad0c6dd8e0bbff492eda15d5ae0f111f4e43905a97fcac3758d102f1b7 +MISC metadata.xml 269 RMD160 53c242e331b0a82669ca7913da16dac854ab8dca SHA1 bc75ba3b0f5607ac5f396d3e8a99daf5ded5a7de SHA256 13472fd0615d2b381dbe36666fe1bbf3b1c34770aa409c6101b38741b4586f85 diff --git a/sci-biology/tablet-bin/files/response.varfile b/sci-biology/tablet-bin/files/response.varfile new file mode 100644 index 000000000..e199cec03 --- /dev/null +++ b/sci-biology/tablet-bin/files/response.varfile @@ -0,0 +1,6 @@ +#install4j response file for Tablet 1.10.09.20 +#Mon Jan 03 23:25:15 CET 2011 +executeLauncherAction$Boolean=false +sys.programGroupDisabled$Boolean=true +sys.languageId=en +sys.installationDir=/var/tmp/portage/sci-biology/tablet-bin-1.10.09.20/image/opt/Tablet diff --git a/sci-biology/tablet-bin/metadata.xml b/sci-biology/tablet-bin/metadata.xml new file mode 100644 index 000000000..07b525505 --- /dev/null +++ b/sci-biology/tablet-bin/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/tablet-bin/tablet-bin-1.10.09.20.ebuild b/sci-biology/tablet-bin/tablet-bin-1.10.09.20.ebuild index b49f41dcd..7f20fb684 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.10.09.20.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.10.09.20.ebuild @@ -1,33 +1,29 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=3 -DESCRIPTION="Tablet is a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments." +DESCRIPTION="Graphical viewer for next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_10_09_20.sh http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" # Tablet uses a modified version of the BSD License which has been edited to remove references to distribution and use in source forms. This means that we are happy for you to distribute and use Tablet however you please, but we do not (yet) want to make the source code publicly available. -LICENSE="BSD-modified" # It's in the installer, and ends up on disk after installation at tablet/docs/tablet.html - # The original BSD licence was modified to remove references to distribution and use in - #source forms, because we cannot make the source code available for Tablet. +LICENSE="Tablet" # It's in the installer, and ends up on disk after installation at /opt/Tablet/docs/tablet.html + # The original BSD licence was modified to remove references to distribution and use in + #source forms, because we cannot make the source code available for Tablet. SLOT="0" -KEYWORDS="~x86 ~amd64" +KEYWORDS="" IUSE="" -DEPEND="dev-lang/java" -RDEPEND="${DEPEND}" +DEPEND="" +RDEPEND="${DEPEND} + virtual/jre + dev-lang/python" src_install() { - sh tablet_linux_x86_1_10_09_20.sh -c -q <<-EOF - o - [Enter] - [Enter] - [Enter] - 1 - "${D}"/opt/Tablet - EOF - dobin "${DISTDIR}"/coveragestats.py | die + # In theory it seems this binary package could be installed through ant instead of the install4j package which is not easy to be forced non-interactive. The below approach is not ideal. + sh "${DISTDIR}"/tablet_linux_x86_1_10_09_20.sh -c -q -overwrite --var-file="${FILESDIR}"/response.varfile --destination="${D}"/opt/Tablet + dobin "${DISTDIR}"/coveragestats.py || die } diff --git a/sci-biology/tclust/metadata.xml b/sci-biology/tclust/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/tclust/metadata.xml +++ b/sci-biology/tclust/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/tgicl/metadata.xml b/sci-biology/tgicl/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/tgicl/metadata.xml +++ b/sci-biology/tgicl/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/tigr-assembler/metadata.xml b/sci-biology/tigr-assembler/metadata.xml index f274f1f44..c07e96e73 100644 --- a/sci-biology/tigr-assembler/metadata.xml +++ b/sci-biology/tigr-assembler/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> <longdescription>TIGR assembler</longdescription> diff --git a/sci-biology/tigr-foundation-libs/metadata.xml b/sci-biology/tigr-foundation-libs/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/tigr-foundation-libs/metadata.xml +++ b/sci-biology/tigr-foundation-libs/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/wcd/metadata.xml b/sci-biology/wcd/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/wcd/metadata.xml +++ b/sci-biology/wcd/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-biology/zmsort/metadata.xml b/sci-biology/zmsort/metadata.xml index d58c0ecd5..07b525505 100644 --- a/sci-biology/zmsort/metadata.xml +++ b/sci-biology/zmsort/metadata.xml @@ -3,7 +3,7 @@ <pkgmetadata> <herd>sci-biology</herd> <maintainer> - <email>mmokrejs@gentoo.org</email> + <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> </pkgmetadata> diff --git a/sci-mathematics/petsc/ChangeLog b/sci-mathematics/petsc/ChangeLog index a275d0512..005db5e1b 100644 --- a/sci-mathematics/petsc/ChangeLog +++ b/sci-mathematics/petsc/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-mathematics/petsc -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*petsc-3.1_p7 (06 Jan 2011) + + 06 Jan 2011; Jens-Malte Gottfried <jmgottfried@web.de> + -petsc-3.1_p5.ebuild, -petsc-3.1_p5-r1.ebuild, +petsc-3.1_p7.ebuild: + added ebuild for recent patchset and removed intermediate ebuilds + 24 Nov 2010; Jens-Malte Gottfried <jmgottfried@web.de> petsc-3.1_p4.ebuild, petsc-3.1_p5.ebuild, petsc-3.1_p5-r1.ebuild, petsc-3.1_p5-r2.ebuild, -files/fix-configure-pic.patch, diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest index 21070fc2e..c86f7a331 100644 --- a/sci-mathematics/petsc/Manifest +++ b/sci-mathematics/petsc/Manifest @@ -2,9 +2,9 @@ AUX petsc-configure-pic.patch 533 RMD160 f24a17f653d67f42cb13701b0798704bcae95ec AUX petsc-disable-rpath.patch 783 RMD160 ed962b20b7cabc6b554b1d9cde3de5c8a120523b SHA1 59ccf94388185c8e54aa7d9772f7616ecc84fe94 SHA256 f92814bf71e6615f8bd0e185c8c9fb06304de705d73a84f234a3f855c104400e DIST petsc-3.1-p4.tar.gz 15455558 RMD160 42d1c587ab1a2676f62de866afe8c43365a1b236 SHA1 4516e74e7ea349fed58b26963cfa3747ef07c62e SHA256 4e9abb2d6a07e49ba77459398871c3f91c50669979f7e9d5017009615d2a24af DIST petsc-3.1-p5.tar.gz 15456384 RMD160 c97e6cf9e000c6eb635a5c76d006b7f8b84b3320 SHA1 e884e3f670093fff66fe1a3964b2f6bfc58543ce SHA256 193c7f8a5826a2bfd47a915f74e87d31a67339f89129aadb16e7b4b9e9dbf7e1 +DIST petsc-3.1-p7.tar.gz 15458474 RMD160 a22f839ae76ad262ff4fa2070fe256fa77a96f06 SHA1 aaee2ddeceb162699ab1b942de6a98c87dcb0b5e SHA256 c13c5eb18955d9c42413406dce8784d8c305d8ed33dcf107db736c309ac20175 EBUILD petsc-3.1_p4.ebuild 4102 RMD160 6dbe234a3b77a1c123df8892352a5c3810e5003d SHA1 46dc5828b917b510a65b72012a88fe2d350559ca SHA256 ec1a91c2025aca456a113702bd4fef0973e61c2fec90c3a413fde12b94b2ae81 -EBUILD petsc-3.1_p5-r1.ebuild 4307 RMD160 7625266411a350c8e61efe13c52817c0dc271b04 SHA1 3ca75c20a100a23377302c9ff069725210a685ff SHA256 9caf737cef3ac45d910c3d8531295936fd0ffc20d07b91d8aca3ffe75096c5b5 EBUILD petsc-3.1_p5-r2.ebuild 4881 RMD160 2294d4569b98bb6db0903e92c99d641143b241dd SHA1 6ed44e1417e88973c575bbdb8afe65a4d5176dc9 SHA256 02465efaf67fd0b8a0ff12e750ccbac7bb76432b399b67528f699c61d8cbd581 -EBUILD petsc-3.1_p5.ebuild 3434 RMD160 6ef6738c04f2ac8da452de53391e9b910befef34 SHA1 82de6bb482de32c5d255eb8c1aacd94b0a6d3a46 SHA256 c8f05d37be66643c94381ca435a47c5ca3505727d0970f9f285388ee123bbf6f -MISC ChangeLog 2018 RMD160 36e5db0c2a1c80edf51264785fef9eaa74ec146a SHA1 7c6cecc0001f2f34e38eb16233ffa6ada40014a3 SHA256 2e1cddc10249e13bea874d86ca55410f4f8e72bd5d2bf1a88c31f5ebff066012 +EBUILD petsc-3.1_p7.ebuild 4881 RMD160 ef5a6585d776f5db34e956754177c24b3d97bd9a SHA1 c0ef05217cba012ae7a54cda908353510d553e00 SHA256 111d150b4243d6a4be72601c99704f1eb7692845ba70069ddbcea795aace197b +MISC ChangeLog 2244 RMD160 dc43f3164304dcecfcf95cfa9fc4a934bee04fdf SHA1 2469ef1280935e118b7fba3d4b031c764e5c8984 SHA256 efa25fb19ee4f157b47ddd265f6f806abd6850b7b188824e9cdfce0e9173d901 MISC metadata.xml 338 RMD160 7bb392dfe214a3ed4048d083323cf5ee5cb10bdb SHA1 e2b7a8a4963ff82d009e5ffcb1a444caaea4262e SHA256 efafc54fd365ea7eee3a0140b197068c8aa2168fefb3a196c091699bf6d18e53 diff --git a/sci-mathematics/petsc/petsc-3.1_p5.ebuild b/sci-mathematics/petsc/petsc-3.1_p5.ebuild deleted file mode 100644 index 1c739b480..000000000 --- a/sci-mathematics/petsc/petsc-3.1_p5.ebuild +++ /dev/null @@ -1,130 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit flag-o-matic toolchain-funcs - -MY_P="${PN}-${PV/_/-}" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/petsc-as/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="petsc" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="mpi X cxx debug static-libs fortran doc" - -RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) - X? ( x11-libs/libX11 ) - virtual/lapack - virtual/blas" - -DEPEND="${RDEPEND} - sys-devel/gcc[-nocxx,fortran?]" - -S="${WORKDIR}/${MY_P}" - -src_prepare(){ - epatch "${FILESDIR}/${PN}-configure-pic.patch" -} - -src_configure(){ - local mylang - local myopt - local myconf - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - export PETSC_DIR="${S}" || die - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" || die - - myconf[10]="--with-blas-lapack-lib=$(pkg-config --libs lapack)" - myconf[11]="CFLAGS=${CFLAGS}" - myconf[12]="CXXFLAGS=${CXXFLAGS}" - myconf[13]="LDFLAGS=${LDFLAGS}" - myconf[14]="--with-windows-graphics=0" - myconf[15]="--with-matlab=0" - myconf[16]="--with-python=0" - myconf[17]="--with-clanguage=${mylang}" - myconf[18]="--with-single-library=1" - myconf[19]="--with-petsc-arch=${PETSC_ARCH}" - myconf[20]="--with-precision=double" - - if use mpi; then - myconf[30]="--with-cc=/usr/bin/mpicc" - myconf[31]="--with-cxx=/usr/bin/mpicxx" - use fortran && myconf[32]="--with-fc=/usr/bin/mpif77" - myconf[33]="--with-mpi=1" - myconf[34]="--with-mpi-compilers=1" - else - myconf[30]="--with-cc=$(tc-getCC)" - myconf[31]="--with-cxx=$(tc-getCXX)" - use fortran && myconf[32]="--with-fc=$(tc-getF77)" - myconf[33]="--with-mpi=0" - fi - - use X \ - && myconf[40]="--with-X=1" \ - || myconf[40]="--with-X=0" - use static-libs \ - && myconf[41]="--with-shared=0" \ - || myconf[41]="--with-shared=1" - use amd64 \ - && myconf[42]="--with-64-bit-indices=1" \ - || myconf[42]="--with-64-bit-indices=0" - use fortran \ - && myconf[43]="--with-fortran=1" \ - || myconf[43]="--with-fortran=0" - - if use debug; then - strip-flags - filter-flags -O* - myconf[44]="--with-debugging=1" - else - myconf[44]="--with-debugging=0" - fi - - python "${S}/config/configure.py" "${myconf[@]}" \ - || die "PETSc configuration failed" -} - -src_install(){ - insinto /usr/include/"${PN}" - doins "${S}"/include/*.h "${S}"/include/*.hh - doins "${S}/${PETSC_ARCH}"/include/*.h - - insinto /usr/include/"${PN}"/private - doins "${S}"/include/private/*.h - - # fix paths stored in petscconf.h - dosed "s:${S}:/usr:g" /usr/include/"${PN}"/petscconf.h - dosed "s:${PETSC_ARCH}/lib:$(get_libdir):g" /usr/include/"${PN}"/petscconf.h \ - - if ! use mpi ; then - insinto /usr/include/"${PN}"/mpiuni - doins "${S}"/include/mpiuni/*.h - fi - - if use doc ; then - dodoc docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi - - use static-libs \ - && dolib.a "${S}/${PETSC_ARCH}"/lib/*.a \ - || dolib.so "${S}/${PETSC_ARCH}"/lib/*.so -} - -pkg_postinst() { - elog "The petsc ebuild is still under development." - elog "Help us improve the ebuild in:" - elog "http://bugs.gentoo.org/show_bug.cgi?id=53386" - elog "This ebuild is known to have parallel build issues, " - elog "hopefully resolved by upstream soon." - elog "Another problem is that you can break this package by" - elog "switching your mpi implementation without rebuild petsc." -} diff --git a/sci-mathematics/petsc/petsc-3.1_p5-r1.ebuild b/sci-mathematics/petsc/petsc-3.1_p7.ebuild index bbf5f78fa..b76ae93df 100644 --- a/sci-mathematics/petsc/petsc-3.1_p5-r1.ebuild +++ b/sci-mathematics/petsc/petsc-3.1_p7.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -15,13 +15,16 @@ SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" LICENSE="petsc" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="mpi hypre X cxx debug static-libs fortran doc" +IUSE="mpi hypre metis hdf5 X cxx debug static-libs fortran doc" RDEPEND="mpi? ( virtual/mpi[cxx?,fortran?] ) X? ( x11-libs/libX11 ) virtual/lapack virtual/blas - hypre? ( >=sci-mathematics/hypre-2.6.0b[static-libs=] )" + hypre? ( >=sci-mathematics/hypre-2.6.0b[static-libs=] ) + metis? ( sci-libs/parmetis ) + hdf5? ( sci-libs/hdf5[!mpi?] ) +" DEPEND="${RDEPEND} sys-devel/gcc[-nocxx,fortran?]" @@ -35,6 +38,7 @@ fi src_prepare(){ epatch "${FILESDIR}/${PN}-configure-pic.patch" + epatch "${FILESDIR}/${PN}-disable-rpath.patch" } src_configure(){ @@ -65,6 +69,9 @@ src_configure(){ || myconf[22]="--with-64-bit-pointers=0" use cxx \ && myconf[23]="--with-c-support=1" + use amd64 \ + && myconf[24]="--with-64-bit-indices=1" \ + || myconf[24]="--with-64-bit-indices=0" if use mpi; then myconf[30]="--with-cc=/usr/bin/mpicc" @@ -99,19 +106,34 @@ src_configure(){ if use hypre; then # hypre cannot handle 64 bit indices, therefore disabled - myconf[51]="--with-64-bit-indices=0" + myconf[24]="--with-64-bit-indices=0" myconf[52]="--with-hypre=1" myconf[53]="--with-hypre-include=/usr/include/hypre" use static-libs \ && myconf[54]="--with-hypre-lib=/usr/$(get_libdir)/libHYPRE.a" \ || myconf[54]="--with-hypre-lib=/usr/$(get_libdir)/libHYPRE.so" else - use amd64 \ - && myconf[51]="--with-64-bit-indices=1" \ - || myconf[51]="--with-64-bit-indices=0" myconf[52]="--with-hypre=0" fi + if use metis; then + myconf[61]="--with-parmetis=1" + myconf[62]="--with-parmetis-include=/usr/include/parmetis" + myconf[63]="--with-parmetis-lib=/usr/$(get_libdir)/libparmetis.so" + else + myconf[61]="--with-parmetis=0" + fi + + if use hdf5; then + myconf[71]="--with-hdf5=1" + myconf[72]="--with-hdf5-include=/usr/include" + myconf[73]="--with-hdf5-lib=/usr/$(get_libdir)/libhdf5.so" + else + myconf[71]="--with-hdf5=0" + fi + + myconf[81]="--with-scotch=0" + einfo "Configure options: ${myconf[@]}" python "${S}/config/configure.py" "${myconf[@]}" \ || die "PETSc configuration failed" |