blob: 6ea39e0adc12316bb3bca66e447d232c60fc72d3 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
|
# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python2_7 )
inherit distutils-r1
DESCRIPTION="Assembly & annotation pipeline with web interface for EST/chromosomal sequences"
HOMEPAGE="http://bioinf.comav.upv.es/ngs_backbone/index.html"
SRC_URI="http://bioinf.comav.upv.es/_downloads/"${P}".tar.gz"
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}
sci-biology/biopython[${PYTHON_USEDEP}]
sci-biology/samtools[${PYTHON_USEDEP}]
sci-biology/picard
sci-biology/mira
sci-biology/bwa
sci-biology/gatk
sci-biology/pysam[${PYTHON_USEDEP}]
sci-biology/estscan
sci-biology/ncbi-tools
sci-biology/lucy
sci-biology/gmap
sci-biology/emboss
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/psubprocess[${PYTHON_USEDEP}]
dev-python/configobj[${PYTHON_USEDEP}]"
# ( blast2GO || b2g4pipe )
# sci-biology/sputnik
# sci-biology/gsnap
# blast2GO is http://www.blast2go.org/home
# a non-GUI pipeline is called b2g4pipe, see https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/b2g4pipe-2-5
# TODO: drop the bundled binaries but ...
# 1. the QA check did not find all bundled binaries, e.g. sputnik, lucy, trimpoly
# 2. until we have them all, maybe keep the installed
#
# * QA Notice: The following files contain writable and executable sections
# * Files with such sections will not work properly (or at all!) on some
# * architectures/operating systems. A bug should be filed at
# * http://bugs.gentoo.org/ to make sure the issue is fixed.
# * For more information, see http://hardened.gentoo.org/gnu-stack.xml
# * Please include the following list of files in your report:
# * Note: Bugs should be filed for the respective maintainers
# * of the package in question and not hardened@g.o.
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
# * RWX --- --- usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bgzip
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastn
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastp
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/blastx
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/bwa
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EBLOSUM62
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/EDNAFULL
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/codes.english
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/est2genome.acd
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/knowntypes.standard
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/emboss_data/water.acd
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/est2genome
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/estscan
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/fa_coords
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_build
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_compress
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_process
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_reassemble
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_setup
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmap_uncompress
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gmapindex
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/gsnap_tally
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/lucy
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/makeblastdb
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/md_coords
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/mdust
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/samtools
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/sputnik
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tabix
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastn
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/tblastx
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/trimpoly
#/usr/lib64/python2.7/site-packages/ext/bin/linux/32bit/water
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bgzip
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastn
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastp
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/blastx
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/bwa
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EBLOSUM62
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/EDNAFULL
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/codes.english
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/est2genome.acd
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/knowntypes.standard
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/emboss_data/water.acd
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/est2genome
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/estscan
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/fa_coords
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_build
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_compress
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_process
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_reassemble
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_setup
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmap_uncompress
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gmapindex
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/gsnap_tally
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/lucy
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/makeblastdb
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/md_coords
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/mdust
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/samtools
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/sputnik
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tabix
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastn
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/tblastx
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/trimpoly
#/usr/lib64/python2.7/site-packages/ext/bin/linux/64bit/water
pkg_postinst(){
einfo "It is highly recommended to install blast2GO. Either the commercial version with GUI"
einfo " or a non-GUI version called b2g4pipe. Either way, refer to http://www.blast2go.org"
einfo " Brief installation process is at http://bioinf.comav.upv.es/ngs_backbone/install.html"
einfo "Alternatively, a VirtualBox image with ngs_bakbone is at http://bioinf.comav.upv.es/_downloads/ngs_machine_v3.tar.gz"
}
|
GitWeb