Mercurial > repos > iuc > package_rsem_1_2_28

comparison tool_dependencies.xml @ 0:987ca85aead4 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rsem_1_2_28 commit 3c4a2b13b0f3a280de4f98f4f5e0dc29e10fc7a0
author iuc
date Tue, 29 Mar 2016 06:33:46 -0400
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-1:000000000000 0:987ca85aead4
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="ncurses" version="6.0">
4 <repository changeset_revision="15e2190c87ca" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="zlib" version="1.2.8">
7 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="rsem" version="1.2.28">
10 <install version="1.0">
11 <actions>
12 <action sha256sum="b54c3ac0ab44b470ab0c29852d30b5194674e36375c3b9067eb3150f569de53e" type="download_by_url">
13 https://github.com/deweylab/RSEM/archive/v1.2.28.tar.gz
14 </action>
15 <action type="set_environment_for_install">
16 <repository changeset_revision="15e2190c87ca" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
17 <package name="ncurses" version="6.0" />
18 </repository>
19 <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
20 <package name="zlib" version="1.2.8" />
21 </repository>
22 </action>
23 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' samtools*/Makefile samtools*/config.mk</action>
24 <action type="shell_command">sed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" Makefile samtools*/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib -->
25 <action type="shell_command">make</action>
26
27 <action type="move_file">
28 <source>rsem-bam2readdepth</source>
29 <destination>$INSTALL_DIR</destination>
30 </action>
31 <action type="move_file">
32 <source>rsem-bam2wig</source>
33 <destination>$INSTALL_DIR</destination>
34 </action>
35 <action type="move_file">
36 <source>rsem-build-read-index</source>
37 <destination>$INSTALL_DIR</destination>
38 </action>
39 <action type="move_file">
40 <source>rsem-calculate-credibility-intervals</source>
41 <destination>$INSTALL_DIR</destination>
42 </action>
43 <action type="move_file">
44 <source>rsem-calculate-expression</source>
45 <destination>$INSTALL_DIR</destination>
46 </action>
47 <action type="move_file">
48 <source>rsem-control-fdr</source>
49 <destination>$INSTALL_DIR</destination>
50 </action>
51 <action type="move_file">
52 <source>rsem-extract-reference-transcripts</source>
53 <destination>$INSTALL_DIR</destination>
54 </action>
55 <action type="move_file">
56 <source>rsem-gen-transcript-plots</source>
57 <destination>$INSTALL_DIR</destination>
58 </action>
59 <action type="move_file">
60 <source>rsem-generate-data-matrix</source>
61 <destination>$INSTALL_DIR</destination>
62 </action>
63 <action type="move_file">
64 <source>rsem-generate-ngvector</source>
65 <destination>$INSTALL_DIR</destination>
66 </action>
67 <action type="move_file">
68 <source>rsem-get-unique</source>
69 <destination>$INSTALL_DIR</destination>
70 </action>
71 <action type="move_file">
72 <source>rsem-gff3-to-gtf</source>
73 <destination>$INSTALL_DIR</destination>
74 </action>
75 <action type="move_file">
76 <source>rsem-parse-alignments</source>
77 <destination>$INSTALL_DIR</destination>
78 </action>
79 <action type="move_file">
80 <source>rsem-plot-model</source>
81 <destination>$INSTALL_DIR</destination>
82 </action>
83 <action type="move_file">
84 <source>rsem-plot-transcript-wiggles</source>
85 <destination>$INSTALL_DIR</destination>
86 </action>
87 <action type="move_file">
88 <source>rsem-prepare-reference</source>
89 <destination>$INSTALL_DIR</destination>
90 </action>
91 <action type="move_file">
92 <source>rsem-preref</source>
93 <destination>$INSTALL_DIR</destination>
94 </action>
95 <action type="move_file">
96 <source>rsem-refseq-extract-primary-assembly</source>
97 <destination>$INSTALL_DIR</destination>
98 </action>
99 <action type="move_file">
100 <source>rsem-run-ebseq</source>
101 <destination>$INSTALL_DIR</destination>
102 </action>
103 <action type="move_file">
104 <source>rsem-run-em</source>
105 <destination>$INSTALL_DIR</destination>
106 </action>
107 <action type="move_file">
108 <source>rsem-run-gibbs</source>
109 <destination>$INSTALL_DIR</destination>
110 </action>
111 <action type="move_file">
112 <source>rsem-sam-validator</source>
113 <destination>$INSTALL_DIR</destination>
114 </action>
115 <action type="move_file">
116 <source>rsem-scan-for-paired-end-reads</source>
117 <destination>$INSTALL_DIR</destination>
118 </action>
119 <action type="move_file">
120 <source>rsem-simulate-reads</source>
121 <destination>$INSTALL_DIR</destination>
122 </action>
123 <action type="move_file">
124 <source>rsem-synthesis-reference-transcripts</source>
125 <destination>$INSTALL_DIR</destination>
126 </action>
127 <action type="move_file">
128 <source>rsem-tbam2gbam</source>
129 <destination>$INSTALL_DIR</destination>
130 </action>
131 <action type="move_file">
132 <source>rsem_perl_utils.pm</source>
133 <destination>$INSTALL_DIR</destination>
134 </action>
135
136 <action type="set_environment">
137 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
138 </action>
139 </actions>
140 </install>
141 </package>
142 </tool_dependency>