Mercurial > repos > mvdbeek > package_sra_toolkit_2_5_2

annotate tool_dependencies.xml @ 7:5f56355f5f7c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
author mvdbeek
date Sun, 25 Oct 2015 18:43:57 -0400
parents 9a412e6be961
children aafba27d2c8a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
1 <?xml version="1.0"?>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
2 <tool_dependency>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
3 <package name="ascp" version="3">
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
4 <repository changeset_revision="e053dbdb5302" name="package_ascp_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu" />
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
5 </package>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
6 <package name="ncbi_vdb" version="2.5.2">
5
aabb60d93e4a planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents: 4
diff changeset
7 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
8 </package>
7
5f56355f5f7c planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 6
diff changeset
9 <package name="ngs_sdk" version="1.1.3">
5f56355f5f7c planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 6
diff changeset
10 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5f56355f5f7c planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 6
diff changeset
11 </package>
6
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
12 <package name="perl" version="5.18.1">
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
13 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
14 </package>
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
15 <package name="sra_toolkit" version="2.5.2">
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
16 <install version="1.0">
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
17 <actions>
6
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
18 <action target_filename="sra-tools-2.5.2.tar.gz" type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
19 <action type="set_environment_for_install">
5
aabb60d93e4a planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents: 4
diff changeset
20 <repository changeset_revision="9e86738381d1" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
21 <package name="ncbi_vdb" version="2.5.2" />
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
22 </repository>
5
aabb60d93e4a planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents: 4
diff changeset
23 <repository changeset_revision="a00c9a1db096" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://testtoolshed.g2.bx.psu.edu">
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
24 <package name="ngs_sdk" version="1.1.3" />
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
25 </repository>
6
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
26 <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
27 <package name="perl" version="5.18.1" />
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
28 </repository>
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
29 </action>
6
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
30 <action type="autoconf">
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
31 --prefix=$INSTALL_DIR -with-ngs-sdk-prefix=$NGS_SDK_DIR --with-ncbi-vdb-sources=$NCBI_VDB_DIR --with-ncbi-vdb-build=$NCBI_VDB_DIR --build=$INSTALL_DIR/build
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
32 </action>
6
9a412e6be961 planemo upload commit d754d6a6fc019236513d2228542fe1a2757d55cf-dirty
mvdbeek
parents: 5
diff changeset
33 <action type="shell_command">sed -i -e "109s/-static//" tools/copycat/Makefile</action>
0
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
34 <action type="make_install" />
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
35 <action type="set_environment">
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
36 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
37 </action>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
38 </actions>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
39 </install>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
40 <readme>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
41 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
42 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
43 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
44 download of a large SRA data set.
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
45
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
46 Build Requirements:
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
47 - make
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
48 - git
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
49 - gcc
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
50 - g++
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
51 - libxml2
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
52 - libcurl4
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
53 - zlib
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
54
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
55 On a debian based Linux OS use:
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
56
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
57 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
58
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
59 </readme>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
60 </package>
d05694dbe2d4 planemo upload commit 92d32947393757598262fbaed175b2c6fd84c181
mvdbeek
parents:
diff changeset
61 </tool_dependency>