Mercurial > repos > stef > qdnaseq

annotate tool_dependencies.xml @ 18:03251c8d6b46 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author stef
date Tue, 17 Jun 2014 04:36:18 -0400
parents 160190da7976
children eefb834376ba
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
8
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
1 <?xml version="1.0"?>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
2 <tool_dependency>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
3
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
4 <set_environment version="1.0">
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
5 <environment_variable name="QDNASEQ_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
6 </set_environment>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
7
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
8 <package name="R" version="3.0.3">
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
9 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/" />
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
10 </package>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
11
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
12 <package name="bioc_qdnaseq" version="1.0.5">
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
13 <install version="1.0">
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
14 <actions>
17
160190da7976 Uploaded
stef
parents: 16
diff changeset
15
160190da7976 Uploaded
stef
parents: 16
diff changeset
16 <action type="shell_command">echo "[DEBUG] BEFORE:" &amp;&amp; pwd</action>
160190da7976 Uploaded
stef
parents: 16
diff changeset
17 <action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
160190da7976 Uploaded
stef
parents: 16
diff changeset
18 <action type="move_file">
18
03251c8d6b46 Uploaded
stef
parents: 17
diff changeset
19 <source>$INSTALL_DIR/QDNAseq.R</source>
03251c8d6b46 Uploaded
stef
parents: 17
diff changeset
20 <destination>./</destination>
17
160190da7976 Uploaded
stef
parents: 16
diff changeset
21 </action>
160190da7976 Uploaded
stef
parents: 16
diff changeset
22
160190da7976 Uploaded
stef
parents: 16
diff changeset
23 <action type="shell_command">echo "[DEBUG] AFTER:" &amp;&amp; pwd</action>
14
7be26321018b Uploaded
stef
parents: 13
diff changeset
24 <action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
15
4472cc10b065 Uploaded
stef
parents: 14
diff changeset
25
8
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
26 <action type="set_environment_for_install">
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
27 <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu/">
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
28 <package name="R" version="3.0.3" />
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
29 </repository>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
30 </action>
13
0a242c6cfdde Uploaded
stef
parents: 12
diff changeset
31 <action type="set_environment">
0a242c6cfdde Uploaded
stef
parents: 12
diff changeset
32 <environment_variable action="prepend_to" name="R_LIBS">$INSTALL_DIR/bin</environment_variable>
0a242c6cfdde Uploaded
stef
parents: 12
diff changeset
33 </action>
15
4472cc10b065 Uploaded
stef
parents: 14
diff changeset
34 <action type="shell_command">echo "[DEBUG] NOW ABOUT TO DOWNLOAD"</action>
11
821fb6bdbbeb Uploaded
stef
parents: 10
diff changeset
35 <action type="shell_command">wget http://bioconductor.org/packages/release/bioc/src/contrib/QDNAseq_1.0.5.tar.gz</action>
14
7be26321018b Uploaded
stef
parents: 13
diff changeset
36
7be26321018b Uploaded
stef
parents: 13
diff changeset
37 <action type="shell_command">echo "[DEBUG] WORKING DIR:" &amp;&amp; pwd</action>
7be26321018b Uploaded
stef
parents: 13
diff changeset
38 <action type="shell_command">echo "[DEBUG] DIR LISTING:" &amp;&amp; ls -l</action>
7be26321018b Uploaded
stef
parents: 13
diff changeset
39
7be26321018b Uploaded
stef
parents: 13
diff changeset
40 <action type="shell_command">echo "[DEBUG] NOW ABOUT TO INSTALL"</action>
12
7318921f937c Uploaded
stef
parents: 11
diff changeset
41 <action type="shell_command">export R_LIBS=$INSTALL_DIR &amp;&amp; R CMD INSTALL --build QDNAseq_1.0.5.tar.gz</action>
9
437bd8b88be2 Uploaded
stef
parents: 8
diff changeset
42 <!--<action type="shell_command">R CMD INSTALL QDNAseq_1.0.5.tar.gz</action>-->
8
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
43 </actions>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
44 </install>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
45
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
46 <readme>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
47 Should install QDNAseq package from bioconductor.
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
48 </readme>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
49 </package>
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
50
b430d4b84233 wget instead of download_by_url
stef
parents:
diff changeset
51 </tool_dependency>