[gentoo-commits] proj/sci:master commit in: sci-biology/est2uni/files/, sci-biology/est2uni/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     ac003e0f4d9835afece6257be187b01fab834460
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 11:00:02 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 11:00:02 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ac003e0f

sci-biology/est2uni: pushing out more patches albeit ugly

(Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)

---
 sci-biology/est2uni/ChangeLog                      |   23 ++++
 sci-biology/est2uni/est2uni-9999.ebuild            |  106 ++++++++++++++++++++
 .../est2uni/files/9999-est_clustering.pm.patch     |   29 ++++++
 sci-biology/est2uni/files/9999-pipe_db.pm.patch    |   15 +++
 4 files changed, 173 insertions(+), 0 deletions(-)

diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog
new file mode 100644
index 0000000..6c7cd1b
--- /dev/null
+++ b/sci-biology/est2uni/ChangeLog
@@ -0,0 +1,23 @@
+# ChangeLog for sci-biology/est2uni
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch,
+  +est2uni-9999.ebuild:
+  ebuild cleanup est2uni-0.27.ebuild est2uni-9999.ebuild Manifest
+  files/9999-est_clustering.pm.patch files/9999-pipe_db.pm.patch
+  files/99est2uni files/est2uni files/est_annot.pm.patch
+  files/est_annot_go.pm.patch files/est_annot_psnp.pm.patch
+  files/est_annot_reciprocal_blast.pm.patch files/est_clustering.pm.patch
+  files/est_prepro.pm.patch files/installation_est2uni_perl.txt.patch
+  files/mysql_fixes.sql files/pipe_db.pm.patch files/tables.sql.patch
+  files/tgicl_files.patch metadata.xml
+
+*est2uni-9999 (05 Jul 2011)
+
+  05 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch,
+  +est2uni-9999.ebuild:
+  vim est2uni-9999.ebuild
+

diff --git a/sci-biology/est2uni/est2uni-9999.ebuild b/sci-biology/est2uni/est2uni-9999.ebuild
new file mode 100644
index 0000000..5066917
--- /dev/null
+++ b/sci-biology/est2uni/est2uni-9999.ebuild
@@ -0,0 +1,106 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit webapp eutils perl-module
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface"
+HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"
+if [ "$PV" == "9999" ]; then
+	EGIT_REPO_URI="git://gitolite@bioinfo.comav.upv.es:2203/est2uni.git"
+	KEYWORDS=""
+else
+	SRC_URI="http://cichlid.umd.edu/est2uni/est2uni.tar.gz
+		ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec
+		ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core
+		http://www.geneontology.org/ontology/gene_ontology.obo
+		http://www.geneontology.org/doc/GO.terms_and_ids"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-3"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sci-biology/lucy
+	sci-biology/cap3-bin
+	sci-biology/estscan
+	<sci-biology/hmmer-3.0
+	sci-biology/phred
+	sci-biology/seqclean
+	sci-biology/repeatmasker
+	sci-biology/tgicl
+	sci-biology/ncbi-tools
+	sci-biology/bioperl
+	sci-biology/exonerate
+	dev-perl/go-perl
+	www-servers/apache
+	>=dev-db/mysql-4.1
+	<dev-lang/php-5.3"
+
+S="${WORKDIR}"/est2uni
+
+src_prepare(){
+	for f in "${FILESDIR}"/9999-*.pm.patch; do
+		cd perl; epatch $f || die "Failed to apply patch $f"
+	done
+}
+
+src_compile(){
+	"$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik
+}
+
+src_install(){
+	mkdir -p "${D}"/opt/est2uni
+	mv external_software/sputnik/sputnik "${D}"/opt/est2uni || die
+
+	chmod a+rx perl/*.pl perl/*.pm || die
+	mv perl/* "${D}"/opt/est2uni || die
+
+	doenvd "${FILESDIR}"/99est2uni || die
+
+	mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs
+	cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die
+
+	mkdir -p "${D}"/opt/est2uni/test_data || die
+	mv test_data/* "${D}"/opt/est2uni/test_data || die
+	# mkdir -p "${D}"/usr/share/"${PN}" || die
+	# mv test_data "${D}"/usr/share/"${PN}" || die
+	perl-module_src_install || die
+
+	webapp_src_preinst
+	webapp_postinst_txt en "${S}"/README
+	webapp_src_install
+	# mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/temp
+	# mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/blast
+
+	# cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die
+
+	einfo "Please follow the pipeline installation and web configuration docs at"
+	einfo "http://cichlid.umd.edu/est2uni/install.php"
+	einfo "BEWARE the software is not maintained anymore by upstream but I do not"
+	einfo "know any better available (replaced by ngs_backbone which has no web"
+	einfo "interface yet). Consider using latest svn checkout instead of 0.27"
+	einfo "release from 2007 or so."
+	einfo "Possible fixes and stuff to read:"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html"
+	einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html"
+	einfo ""
+	einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary"
+}
+
+pkg_postinst(){
+	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+}

diff --git a/sci-biology/est2uni/files/9999-est_clustering.pm.patch b/sci-biology/est2uni/files/9999-est_clustering.pm.patch
new file mode 100644
index 0000000..ec38e52
--- /dev/null
+++ b/sci-biology/est2uni/files/9999-est_clustering.pm.patch
@@ -0,0 +1,29 @@
+--- perl/est_prepro.pm.ori	2011-02-23 10:56:06.000000000 +0100
++++ perl/est_prepro.pm	2011-02-23 19:53:13.000000000 +0100
+@@ -499,15 +499,17 @@
+ 					$sth->bind_param(5,$unique_seq_control);
+ 					# we get the clone names from the data file
+ 					# if not in the data file, we guess it following user specifications in config file
+-					unless (${%$clone}{$real_name}) {
+-						${%$clone}{$real_name}=get_clone_from_est($config,$real_name);
+-					}
+-					$sth->bind_param(6,${%$clone}{$real_name});
+-					$$seq_info{clone}=${%$clone}{$real_name};
+-					if (!${%$clone}{$real_name}){
+-						print localtime().": Unable to get clone name for EST $real_name\n";
+-						return undef;
+-					}
++					#unless (${%$clone}{$real_name}) {
++					#	${%$clone}{$real_name}=get_clone_from_est($config,$real_name);
++					#}
++					#$sth->bind_param(6,${%$clone}{$real_name});
++					#$$seq_info{clone}=${%$clone}{$real_name};
++					#if (!${%$clone}{$real_name}){
++					#	print localtime().": Unable to get clone name for EST $real_name\n";
++					#	return undef;
++					#}
++					$sth->bind_param(6,'blah');
++					$$seq_info{clone}='blah';
+ 				}
+ 				if (not $qual and not ($unique_seq_control eq 'raw_est' or $unique_seq_control eq 'clean_est')) {
+ 					$sth->bind_param(5,$unique_seq_control)

diff --git a/sci-biology/est2uni/files/9999-pipe_db.pm.patch b/sci-biology/est2uni/files/9999-pipe_db.pm.patch
new file mode 100644
index 0000000..729c550
--- /dev/null
+++ b/sci-biology/est2uni/files/9999-pipe_db.pm.patch
@@ -0,0 +1,15 @@
+--- perl/pipe_db.pm	2011-02-23 18:38:47.000000000 +0100
++++ pipe_db.pm	2011-02-23 19:41:06.000000000 +0100
+@@ -1468,10 +1468,11 @@
+ 	my $tables=shift;
+ 	my $ok=1;
+ 
++	my %t = %$tables; # Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1474.
+ 	my $table;
+ 	foreach $table(keys %$tables) {
+ 		if ($ok) {
+-			$ok=create_table($db,$table,${%{$tables}}{$table});
++			$ok=create_table($db,$table,$t{$table});
+ 			if ($ok) {
+ 				print localtime().": Table $table created\n";
+ 			} else {