Gentoo Archives: gentoo-commits

From: Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
To: gentoo-commits@l.g.o
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/est2uni/files/, sci-biology/est2uni/
Date: Sat, 30 Jul 2011 11:02:58
Message-Id: ac003e0f4d9835afece6257be187b01fab834460.mmokrejs@gentoo
1 commit: ac003e0f4d9835afece6257be187b01fab834460
2 Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
3 AuthorDate: Sat Jul 30 11:00:02 2011 +0000
4 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
5 CommitDate: Sat Jul 30 11:00:02 2011 +0000
6 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ac003e0f
7
8 sci-biology/est2uni: pushing out more patches albeit ugly
9
10 (Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit)
11
12 ---
13 sci-biology/est2uni/ChangeLog | 23 ++++
14 sci-biology/est2uni/est2uni-9999.ebuild | 106 ++++++++++++++++++++
15 .../est2uni/files/9999-est_clustering.pm.patch | 29 ++++++
16 sci-biology/est2uni/files/9999-pipe_db.pm.patch | 15 +++
17 4 files changed, 173 insertions(+), 0 deletions(-)
18
19 diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog
20 new file mode 100644
21 index 0000000..6c7cd1b
22 --- /dev/null
23 +++ b/sci-biology/est2uni/ChangeLog
24 @@ -0,0 +1,23 @@
25 +# ChangeLog for sci-biology/est2uni
26 +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
27 +# $Header: $
28 +
29 + 30 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
30 + +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch,
31 + +est2uni-9999.ebuild:
32 + ebuild cleanup est2uni-0.27.ebuild est2uni-9999.ebuild Manifest
33 + files/9999-est_clustering.pm.patch files/9999-pipe_db.pm.patch
34 + files/99est2uni files/est2uni files/est_annot.pm.patch
35 + files/est_annot_go.pm.patch files/est_annot_psnp.pm.patch
36 + files/est_annot_reciprocal_blast.pm.patch files/est_clustering.pm.patch
37 + files/est_prepro.pm.patch files/installation_est2uni_perl.txt.patch
38 + files/mysql_fixes.sql files/pipe_db.pm.patch files/tables.sql.patch
39 + files/tgicl_files.patch metadata.xml
40 +
41 +*est2uni-9999 (05 Jul 2011)
42 +
43 + 05 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
44 + +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch,
45 + +est2uni-9999.ebuild:
46 + vim est2uni-9999.ebuild
47 +
48
49 diff --git a/sci-biology/est2uni/est2uni-9999.ebuild b/sci-biology/est2uni/est2uni-9999.ebuild
50 new file mode 100644
51 index 0000000..5066917
52 --- /dev/null
53 +++ b/sci-biology/est2uni/est2uni-9999.ebuild
54 @@ -0,0 +1,106 @@
55 +# Copyright 1999-2011 Gentoo Foundation
56 +# Distributed under the terms of the GNU General Public License v2
57 +# $Header: $
58 +
59 +EAPI=3
60 +
61 +inherit webapp eutils perl-module
62 +
63 +[ "$PV" == "9999" ] && inherit git-2
64 +
65 +DESCRIPTION="EST assembly+annotation: a perl-based analysis pipeline including php-based web interface"
66 +HOMEPAGE="http://cichlid.umd.edu/est2uni/download.php"
67 +if [ "$PV" == "9999" ]; then
68 + EGIT_REPO_URI="git://gitolite@×××××××××××××××××.es:2203/est2uni.git"
69 + KEYWORDS=""
70 +else
71 + SRC_URI="http://cichlid.umd.edu/est2uni/est2uni.tar.gz
72 + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec
73 + ftp://ftp.ncbi.nih.gov/pub/UniVec/UniVec_Core
74 + http://www.geneontology.org/ontology/gene_ontology.obo
75 + http://www.geneontology.org/doc/GO.terms_and_ids"
76 + KEYWORDS="~amd64 ~x86"
77 +fi
78 +
79 +LICENSE="GPL-3"
80 +IUSE=""
81 +
82 +DEPEND=""
83 +RDEPEND="${DEPEND}
84 + sci-biology/lucy
85 + sci-biology/cap3-bin
86 + sci-biology/estscan
87 + <sci-biology/hmmer-3.0
88 + sci-biology/phred
89 + sci-biology/seqclean
90 + sci-biology/repeatmasker
91 + sci-biology/tgicl
92 + sci-biology/ncbi-tools
93 + sci-biology/bioperl
94 + sci-biology/exonerate
95 + dev-perl/go-perl
96 + www-servers/apache
97 + >=dev-db/mysql-4.1
98 + <dev-lang/php-5.3"
99 +
100 +S="${WORKDIR}"/est2uni
101 +
102 +src_prepare(){
103 + for f in "${FILESDIR}"/9999-*.pm.patch; do
104 + cd perl; epatch $f || die "Failed to apply patch $f"
105 + done
106 +}
107 +
108 +src_compile(){
109 + "$(tc-getCC)" external_software/sputnik/sputnik.c -o external_software/sputnik/sputnik
110 +}
111 +
112 +src_install(){
113 + mkdir -p "${D}"/opt/est2uni
114 + mv external_software/sputnik/sputnik "${D}"/opt/est2uni || die
115 +
116 + chmod a+rx perl/*.pl perl/*.pm || die
117 + mv perl/* "${D}"/opt/est2uni || die
118 +
119 + doenvd "${FILESDIR}"/99est2uni || die
120 +
121 + mkdir -p "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs
122 + cp -r php/* "${D}"/usr/share/webapps/"${PN}"/"${PV}"/htdocs || die
123 +
124 + mkdir -p "${D}"/opt/est2uni/test_data || die
125 + mv test_data/* "${D}"/opt/est2uni/test_data || die
126 + # mkdir -p "${D}"/usr/share/"${PN}" || die
127 + # mv test_data "${D}"/usr/share/"${PN}" || die
128 + perl-module_src_install || die
129 +
130 + webapp_src_preinst
131 + webapp_postinst_txt en "${S}"/README
132 + webapp_src_install
133 + # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/temp
134 + # mkdir -p /var/www/localhost/htdocs/est2uni/est2uni/blast
135 +
136 + # cp "${DISTDIR}"/UniVec_Core "${DISTDIR}"/UniVec "${D}"/usr/share/ncbi/data/ || die
137 +
138 + einfo "Please follow the pipeline installation and web configuration docs at"
139 + einfo "http://cichlid.umd.edu/est2uni/install.php"
140 + einfo "BEWARE the software is not maintained anymore by upstream but I do not"
141 + einfo "know any better available (replaced by ngs_backbone which has no web"
142 + einfo "interface yet). Consider using latest svn checkout instead of 0.27"
143 + einfo "release from 2007 or so."
144 + einfo "Possible fixes and stuff to read:"
145 + einfo "https://listas.upv.es/pipermail/est2uni/2008-January/000069.html"
146 + einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000103.html"
147 + einfo "https://listas.upv.es/pipermail/est2uni/2008-March/000101.html"
148 + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000135.html"
149 + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000131.html"
150 + einfo "https://listas.upv.es/pipermail/est2uni/2008-February/000070.html"
151 + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000129.html"
152 + einfo "https://listas.upv.es/pipermail/est2uni/2008-April/000128.html"
153 + einfo "https://listas.upv.es/pipermail/est2uni/2008-May/000139.html"
154 + einfo ""
155 + einfo "Current code is at http://bioinf.comav.upv.es/git///?p=est2uni;a=summary"
156 +}
157 +
158 +pkg_postinst(){
159 + webapp_pkg_postinst || die "webapp_pkg_postinst failed"
160 +}
161
162 diff --git a/sci-biology/est2uni/files/9999-est_clustering.pm.patch b/sci-biology/est2uni/files/9999-est_clustering.pm.patch
163 new file mode 100644
164 index 0000000..ec38e52
165 --- /dev/null
166 +++ b/sci-biology/est2uni/files/9999-est_clustering.pm.patch
167 @@ -0,0 +1,29 @@
168 +--- perl/est_prepro.pm.ori 2011-02-23 10:56:06.000000000 +0100
169 ++++ perl/est_prepro.pm 2011-02-23 19:53:13.000000000 +0100
170 +@@ -499,15 +499,17 @@
171 + $sth->bind_param(5,$unique_seq_control);
172 + # we get the clone names from the data file
173 + # if not in the data file, we guess it following user specifications in config file
174 +- unless (${%$clone}{$real_name}) {
175 +- ${%$clone}{$real_name}=get_clone_from_est($config,$real_name);
176 +- }
177 +- $sth->bind_param(6,${%$clone}{$real_name});
178 +- $$seq_info{clone}=${%$clone}{$real_name};
179 +- if (!${%$clone}{$real_name}){
180 +- print localtime().": Unable to get clone name for EST $real_name\n";
181 +- return undef;
182 +- }
183 ++ #unless (${%$clone}{$real_name}) {
184 ++ # ${%$clone}{$real_name}=get_clone_from_est($config,$real_name);
185 ++ #}
186 ++ #$sth->bind_param(6,${%$clone}{$real_name});
187 ++ #$$seq_info{clone}=${%$clone}{$real_name};
188 ++ #if (!${%$clone}{$real_name}){
189 ++ # print localtime().": Unable to get clone name for EST $real_name\n";
190 ++ # return undef;
191 ++ #}
192 ++ $sth->bind_param(6,'blah');
193 ++ $$seq_info{clone}='blah';
194 + }
195 + if (not $qual and not ($unique_seq_control eq 'raw_est' or $unique_seq_control eq 'clean_est')) {
196 + $sth->bind_param(5,$unique_seq_control)
197
198 diff --git a/sci-biology/est2uni/files/9999-pipe_db.pm.patch b/sci-biology/est2uni/files/9999-pipe_db.pm.patch
199 new file mode 100644
200 index 0000000..729c550
201 --- /dev/null
202 +++ b/sci-biology/est2uni/files/9999-pipe_db.pm.patch
203 @@ -0,0 +1,15 @@
204 +--- perl/pipe_db.pm 2011-02-23 18:38:47.000000000 +0100
205 ++++ pipe_db.pm 2011-02-23 19:41:06.000000000 +0100
206 +@@ -1468,10 +1468,11 @@
207 + my $tables=shift;
208 + my $ok=1;
209 +
210 ++ my %t = %$tables; # Can't use string ("38/64") as a HASH ref while "strict refs" in use at /opt/est2uni/pipe_db.pm line 1474.
211 + my $table;
212 + foreach $table(keys %$tables) {
213 + if ($ok) {
214 +- $ok=create_table($db,$table,${%{$tables}}{$table});
215 ++ $ok=create_table($db,$table,$t{$table});
216 + if ($ok) {
217 + print localtime().": Table $table created\n";
218 + } else {