Mercurial > repos > rnateam > blockclust

comparison tool_dependencies.xml @ 0:768a67f6ae18 draft

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author rnateam
date Tue, 06 May 2014 07:49:25 -0400
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-1:000000000000 0:768a67f6ae18
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="samtools" version="0.1.19">
4 <repository changeset_revision="6b6b5498d9a2" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="R_3_0_1" version="3.0.1">
7 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
8 </package>
9 <package name="eden" version="1.1">
10 <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="http://toolshed.g2.bx.psu.edu" />
11 </package>
12 <package name="mcl" version="12.135">
13 <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="http://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="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
20 <package name="R_3_0_1" version="3.0.1" />
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/scales_0.2.3.tar.gz</package>
31 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz</package>
32 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz</package>
33 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
34 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz</package>
35 </action>
36 </actions>
37 </install>
38 <readme>
39
40 </readme>
41 </package>
42 <package name="blockclust" version="1.0">
43 <install version="1.0">
44 <actions>
45 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
46 <action type="shell_command">make</action>
47 <action type="move_file">
48 <source>BlockClust</source>
49 <destination>$INSTALL_DIR/bin</destination>
50 </action>
51 <action type="move_file">
52 <source>BlockClustPipeLine.pl</source>
53 <destination>$INSTALL_DIR/bin</destination>
54 </action>
55 <action type="move_file">
56 <source>perf</source>
57 <destination>$INSTALL_DIR/bin</destination>
58 </action>
59 <action type="move_file">
60 <source>plotClusters.R</source>
61 <destination>$INSTALL_DIR/bin</destination>
62 </action>
63 <action type="move_file">
64 <source>blockclust.config</source>
65 <destination>$INSTALL_DIR/data/</destination>
66 </action>
67 <action type="move_file">
68 <source>rfam_map.txt</source>
69 <destination>$INSTALL_DIR/data/</destination>
70 </action>
71 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
72 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
73 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
74 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
75 <action type="shell_command">tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
76 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
77 <action type="shell_command">tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
78 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
79 <action type="shell_command">tar xfvz panTro4.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/rheMac3.tar.gz</action>
81 <action type="shell_command">tar xfvz rheMac3.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/celWS235.tar.gz</action>
83 <action type="shell_command">tar xfvz celWS235.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/tair10.tar.gz</action>
85 <action type="shell_command">tar xfvz tair10.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/models.tar.gz</action>
87 <action type="shell_command">tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action>
88 <action type="set_environment">
89 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
90 <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
91 </action>
92 </actions>
93 </install>
94 <readme>
95
96 </readme>
97 </package>
98 </tool_dependency>