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commit: ac003e0f4d9835afece6257be187b01fab834460 |
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Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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AuthorDate: Sat Jul 30 11:00:02 2011 +0000 |
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Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> |
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CommitDate: Sat Jul 30 11:00:02 2011 +0000 |
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URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ac003e0f |
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|
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sci-biology/est2uni: pushing out more patches albeit ugly |
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|
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(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit) |
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|
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--- |
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sci-biology/est2uni/ChangeLog | 23 ++++ |
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sci-biology/est2uni/est2uni-9999.ebuild | 106 ++++++++++++++++++++ |
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.../est2uni/files/9999-est_clustering.pm.patch | 29 ++++++ |
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sci-biology/est2uni/files/9999-pipe_db.pm.patch | 15 +++ |
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4 files changed, 173 insertions(+), 0 deletions(-) |
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|
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diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog |
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new file mode 100644 |
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index 0000000..6c7cd1b |
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--- /dev/null |
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+++ b/sci-biology/est2uni/ChangeLog |
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@@ -0,0 +1,23 @@ |
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+# ChangeLog for sci-biology/est2uni |
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+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 |
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+# $Header: $ |
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+ |
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+ 30 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, |
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+ +est2uni-9999.ebuild: |
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+ ebuild cleanup est2uni-0.27.ebuild est2uni-9999.ebuild Manifest |
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+ files/9999-est_clustering.pm.patch files/9999-pipe_db.pm.patch |
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+ files/99est2uni files/est2uni files/est_annot.pm.patch |
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+ files/est_annot_go.pm.patch files/est_annot_psnp.pm.patch |
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+ files/est_annot_reciprocal_blast.pm.patch files/est_clustering.pm.patch |
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+ files/est_prepro.pm.patch files/installation_est2uni_perl.txt.patch |
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+ files/mysql_fixes.sql files/pipe_db.pm.patch files/tables.sql.patch |
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+ files/tgicl_files.patch metadata.xml |
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+ |
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+*est2uni-9999 (05 Jul 2011) |
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+ |
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+ 05 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> |
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+ +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, |
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+ +est2uni-9999.ebuild: |
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+ vim est2uni-9999.ebuild |
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+ |
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|
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diff --git a/sci-biology/est2uni/est2uni-9999.ebuild b/sci-biology/est2uni/est2uni-9999.ebuild |
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new file mode 100644 |
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index 0000000..5066917 |
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--- /dev/null |
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+++ b/sci-biology/est2uni/est2uni-9999.ebuild |
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@@ -0,0 +1,106 @@ |
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+# Copyright 1999-2011 Gentoo Foundation |
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+# Distributed under the terms of the GNU General Public License v2 |
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+# $Header: $ |
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+ |
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+EAPI=3 |
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+ |
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+inherit webapp eutils perl-module |
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+ |
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+[ "$PV" == "9999" ] && inherit git-2 |
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+ |
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+DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface" |
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+HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php" |
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+if [ "$PV" == "9999" ]; then |
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+ EGIT_REPO_URI="git://gitolite@×××××××××××××××××.es:2203/est2uni.git" |
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+ KEYWORDS="" |
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+else |
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+ SRC_URI="http://cichlid.umd.edu/est2uni/est2uni.tar.gz |
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+ ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec |
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+ ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core |
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+ http://www.geneontology.org/ontology/gene_ontology.obo |
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+ http://www.geneontology.org/doc/GO.terms_and_ids" |
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+ KEYWORDS="~amd64 ~x86" |
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+fi |
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+ |
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+LICENSE="GPL-3" |
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+IUSE="" |
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+ |
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+DEPEND="" |
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+RDEPEND="${DEPEND} |
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+ sci-biology/lucy |
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+ sci-biology/cap3-bin |
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+ sci-biology/estscan |
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+ <sci-biology/hmmer-3.0 |
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+ sci-biology/phred |
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+ sci-biology/seqclean |
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+ sci-biology/repeatmasker |
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+ sci-biology/tgicl |
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+ sci-biology/ncbi-tools |
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+ sci-biology/bioperl |
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+ sci-biology/exonerate |
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+ dev-perl/go-perl |
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+ www-servers/apache |
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+ >=dev-db/mysql-4.1 |
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+ <dev-lang/php-5.3" |
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+ |
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+S="${WORKDIR}"/est2uni |
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+ |
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+src_prepare(){ |
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+ for f in "${FILESDIR}"/9999-*.pm.patch; do |
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+ cd perl; epatch $f || die "Failed to apply patch $f" |
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+ done |
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+} |
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+ |
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+src_compile(){ |
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+ "$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik |
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+} |
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+ |
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+src_install(){ |
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+ mkdir -p "${D}"/opt/est2uni |
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+ mv external_software/sputnik/sputnik "${D}"/opt/est2uni || die |
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+ |
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+ chmod a+rx perl/*.pl perl/*.pm || die |
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+ mv perl/* "${D}"/opt/est2uni || die |
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+ |
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+ doenvd "${FILESDIR}"/99est2uni || die |
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+ |
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+ mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs |
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+ cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die |
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+ |
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+ mkdir -p "${D}"/opt/est2uni/test_data || die |
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+ mv test_data/* "${D}"/opt/est2uni/test_data || die |
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+ # mkdir -p "${D}"/usr/share/"${PN}" || die |
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+ # mv test_data "${D}"/usr/share/"${PN}" || die |
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+ perl-module_src_install || die |
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+ |
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+ webapp_src_preinst |
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+ webapp_postinst_txt en "${S}"/README |
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+ webapp_src_install |
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+ # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/temp |
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+ # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/blast |
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+ |
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+ # cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die |
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+ |
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+ einfo "Please follow the pipeline installation and web configuration docs at" |
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+ einfo "http://cichlid.umd.edu/est2uni/install.php" |
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+ einfo "BEWARE the software is not maintained anymore by upstream but I do not" |
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+ einfo "know any better available (replaced by ngs_backbone which has no web" |
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+ einfo "interface yet). Consider using latest svn checkout instead of 0.27" |
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+ einfo "release from 2007 or so." |
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+ einfo "Possible fixes and stuff to read:" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html" |
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+ einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html" |
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+ einfo "" |
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+ einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary" |
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+} |
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+ |
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+pkg_postinst(){ |
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+ webapp_pkg_postinst || die "webapp_pkg_postinst failed" |
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+} |
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|
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diff --git a/sci-biology/est2uni/files/9999-est_clustering.pm.patch b/sci-biology/est2uni/files/9999-est_clustering.pm.patch |
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new file mode 100644 |
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index 0000000..ec38e52 |
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--- /dev/null |
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+++ b/sci-biology/est2uni/files/9999-est_clustering.pm.patch |
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@@ -0,0 +1,29 @@ |
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+--- perl/est_prepro.pm.ori 2011-02-23 10:56:06.000000000 +0100 |
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++++ perl/est_prepro.pm 2011-02-23 19:53:13.000000000 +0100 |
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+@@ -499,15 +499,17 @@ |
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+ $sth->bind_param(5,$unique_seq_control); |
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+ # we get the clone names from the data file |
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+ # if not in the data file, we guess it following user specifications in config file |
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+- unless (${%$clone}{$real_name}) { |
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+- ${%$clone}{$real_name}=get_clone_from_est($config,$real_name); |
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+- } |
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+- $sth->bind_param(6,${%$clone}{$real_name}); |
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+- $$seq_info{clone}=${%$clone}{$real_name}; |
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+- if (!${%$clone}{$real_name}){ |
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+- print localtime().": Unable to get clone name for EST $real_name\n"; |
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+- return undef; |
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+- } |
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++ #unless (${%$clone}{$real_name}) { |
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++ # ${%$clone}{$real_name}=get_clone_from_est($config,$real_name); |
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++ #} |
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++ #$sth->bind_param(6,${%$clone}{$real_name}); |
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++ #$$seq_info{clone}=${%$clone}{$real_name}; |
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++ #if (!${%$clone}{$real_name}){ |
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++ # print localtime().": Unable to get clone name for EST $real_name\n"; |
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++ # return undef; |
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++ #} |
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++ $sth->bind_param(6,'blah'); |
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++ $$seq_info{clone}='blah'; |
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+ } |
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+ if (not $qual and not ($unique_seq_control eq 'raw_est' or $unique_seq_control eq 'clean_est')) { |
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+ $sth->bind_param(5,$unique_seq_control) |
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|
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diff --git a/sci-biology/est2uni/files/9999-pipe_db.pm.patch b/sci-biology/est2uni/files/9999-pipe_db.pm.patch |
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new file mode 100644 |
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index 0000000..729c550 |
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--- /dev/null |
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+++ b/sci-biology/est2uni/files/9999-pipe_db.pm.patch |
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@@ -0,0 +1,15 @@ |
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+--- perl/pipe_db.pm 2011-02-23 18:38:47.000000000 +0100 |
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++++ pipe_db.pm 2011-02-23 19:41:06.000000000 +0100 |
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+@@ -1468,10 +1468,11 @@ |
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+ my $tables=shift; |
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+ my $ok=1; |
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+ |
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++ my %t = %$tables; # Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1474. |
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+ my $table; |
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+ foreach $table(keys %$tables) { |
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+ if ($ok) { |
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+- $ok=create_table($db,$table,${%{$tables}}{$table}); |
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++ $ok=create_table($db,$table,$t{$table}); |
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+ if ($ok) { |
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+ print localtime().": Table $table created\n"; |
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+ } else { |