Mercurial > repos > jjohnson > shear

annotate tool_dependencies.xml @ 8:8fac6c7d32fd

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Copy reference fasta for shear sv to avoid GATK issue with symlinks
author Jim Johnson <jj@umn.edu>
date Tue, 22 Oct 2013 09:44:32 -0500
parents 8180f6b0249b
children 2620f7984418
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
1 <?xml version="1.0"?>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
2 <tool_dependency>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
3 <package name="samtools" version="0.1.18">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
4 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
5 </package>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
6 <package name="bwa" version="0.6.2">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
7 <repository changeset_revision="8be5fbfc1548" name="package_bwa_0_6_2" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
8 </package>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
9 <package name="kent" version="latest">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
10 <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
11 </package>
7
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
12 <package name="cap3" version="3">
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
13 <repository changeset_revision="a472ccd208e2" name="package_cap3_3" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
14 </package>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
15 <package name="crest" version="1.0.1">
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
16 <repository changeset_revision="89a9d6ce7f96" name="package_crest_1_0_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
17 <readme>
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
18 CREST requires:
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
19 Bioperl package Bio::DB:Sam
7
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
20 blat - requires license for commercial use
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
21 cap3 - requires license for commercial use
4
a82400332451 Use shear_wrapper.py to generate reference indexes when needed
Jim Johnson <jj@umn.edu>
parents: 0
diff changeset
22 </readme>
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
23 </package>
7
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
24 <package name="shear" version="0.2.4">
8180f6b0249b Upgrade to SHEAR version 0.2.4
Jim Johnson <jj@umn.edu>
parents: 5
diff changeset
25 <repository changeset_revision="d6a7b8497a7b" name="package_shear_0_2_4" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
0
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
26 </package>
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
27
ea76da1e7281 Uploaded
jjohnson
parents:
diff changeset
28 </tool_dependency>