Mercurial > repos > bgruening > blockclust

comparison tool_dependencies.xml @ 0:5365d08bead0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/blockclust commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author bgruening
date Thu, 17 Sep 2015 16:49:52 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:5365d08bead0
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="R" version="3.0.3">
7 <repository changeset_revision="6ce19fda3a9a" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="eden" version="1.1">
10 <repository changeset_revision="767f6e9800dd" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="mcl" version="12.135">
13 <repository changeset_revision="7003196be1b1" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
14 </package>
15 <package name="blockclust_rlibs" version="1.0">
16 <install version="1.0">
17 <actions>
18 <action type="setup_r_environment">
19 <repository changeset_revision="6ce19fda3a9a" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
20 <package name="R" version="3.0.3" />
21 </repository>
22 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package>
23 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz</package>
24 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz</package>
25 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz</package>
26 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz</package>
27 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz</package>
28 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz</package>
29 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz</package>
30 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/RColorBrewer_1.0-5.tar.gz</package>
31 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/stringr_0.6.2.tar.gz</package>
32 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz</package>
33 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz</package>
34 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz</package>
35 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
36 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz</package>
37 </action>
38 </actions>
39 </install>
40 <readme>
41
42 </readme>
43 </package>
44 <package name="blockclust" version="1.0">
45 <install version="1.0">
46 <actions>
47 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
48 <action type="shell_command">make</action>
49 <action type="move_file">
50 <source>BlockClust</source>
51 <destination>$INSTALL_DIR/bin</destination>
52 </action>
53 <action type="move_file">
54 <source>BlockClustPipeLine.pl</source>
55 <destination>$INSTALL_DIR/bin</destination>
56 </action>
57 <action type="move_file">
58 <source>filterKnownBlockGroups.pl</source>
59 <destination>$INSTALL_DIR/bin</destination>
60 </action>
61 <action type="move_file">
62 <source>perf</source>
63 <destination>$INSTALL_DIR/bin</destination>
64 </action>
65 <action type="move_file">
66 <source>plotClusters.R</source>
67 <destination>$INSTALL_DIR/bin</destination>
68 </action>
69 <action type="move_file">
70 <source>blockclust.config</source>
71 <destination>$INSTALL_DIR/data/</destination>
72 </action>
73 <action type="move_file">
74 <source>rfam_map.txt</source>
75 <destination>$INSTALL_DIR/data/</destination>
76 </action>
77 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
78 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
79 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
80 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
81 <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
82 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
83 <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
84 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
85 <action type="shell_command">tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
86 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
87 <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
88 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action>
89 <action type="shell_command">tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action>
90 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action>
91 <action type="shell_command">tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
92 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action>
93 <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action>
94 <action type="set_environment">
95 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
96 <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
97 </action>
98 </actions>
99 </install>
100 <readme>
101
102 </readme>
103 </package>
104 </tool_dependency>