annotate tool_dependencies.xml @ 2:95cffefc0dfe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
author iuc
date Wed, 15 Jun 2016 06:22:39 -0400
parents 0beed64123fb
children 51d4ab2c4dcf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
2 <tool_dependency>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
3 <package name="samtools" version="0.1.19">
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
4 <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
5 </package>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
6 <package name="stacks" version="1.40">
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
7 <install version="1.0">
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
8 <actions>
1
0beed64123fb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 64069b03d33644632275cb79a017f5425323c75e
iuc
parents: 0
diff changeset
9 <action sha256sum="bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493" type="download_by_url">https://depot.galaxyproject.org/software/stacks/stacks_1.40_src_all.tar.gz</action>
2
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
10
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
11 <action type="set_environment_for_install">
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
12 <repository changeset_revision="96aab723499f" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
13 <package name="samtools" version="0.1.19" />
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
14 </repository>
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
15 </action>
95cffefc0dfe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit 6b38bb0f0d7e65b01680a4b56bf8a996c445e58f
iuc
parents: 1
diff changeset
16
0
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
17 <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_ROOT}/include/bam --with-bam-lib-path=${BAM_LIB_PATH}</action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
18 <action type="shell_command">make</action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
19 <action type="shell_command">make install</action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
20 <!-- create env.sh -->
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
21 <action type="set_environment">
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
22 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
23 <environment_variable action="set_to" name="STACKS_ROOT_DIR">$INSTALL_DIR/</environment_variable>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
24 </action>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
25 </actions>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
26 </install>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
27 <readme>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
28 This package installs STACKS from the sources available. Based on Cyril Monjeuad version
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
29 </readme>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
30 </package>
5eac5e2d91e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit f3a59c91c231cc1582479109e776d05602b7f24d-dirty
iuc
parents:
diff changeset
31 </tool_dependency>