Mercurial > repos > lionelguy > spades

annotate tools/spades_2_5/tool_dependencies.xml @ 3:d82f18c76309 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
author lionelguy
date Thu, 12 Sep 2013 07:46:54 -0400
parents 0f8b2da62d7d
children 1b1af74a54ae
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
1 <?xml version="1.0"?>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
2 <tool_dependency>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
3 <package name="spades" version="2.5.0">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
4 <install version="1.0">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
5 <actions>
3
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
6 <action type="download_by_url">http://spades.bioinf.spbau.ru/release2.5.1/SPAdes-2.5.1-Linux.tar.gz</action>
1
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
7 <!-- Copying the whole bin folder -->
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
8 <action type="make_directory">$INSTALL_DIR/bin</action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
9 <action type="make_directory">$INSTALL_DIR/share</action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
10 <action type="move_directory_files">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
11 <source_directory>bin</source_directory>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
13 </action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
14 <action type="move_directory_files">
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
15 <source_directory>share</source_directory>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
16 <destination_directory>$INSTALL_DIR/share</destination_directory>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
17 </action>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
18 <!-- This is required to have spades accept .dat files -->
3
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
19 <!-- <action type="shell_command">sed -i -e "s/\('\.fa', '\.fasta', '\.fq', '\.fastq', '\.gz'\)/\\1, '.dat'/" $INSTALL_DIR/share/spades/spades_pipeline/support.py</action> -->
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
20 <!-- <action type="set_environment"> -->
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
21 <!-- <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> -->
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
22 <!-- </action> -->
1
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
23 </actions>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
24 </install>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
25 <readme>
3
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
26 This installs SPAdes 2.5.1.
1
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
27
3
d82f18c76309 Uploaded spades wrapper 0.6. Supports spades 2.5.1. Also removes the need for the hack at installation time, by fixing the problem with input files. Shows the license for the tool as well.
lionelguy
parents: 1
diff changeset
28 See manual here http://spades.bioinf.spbau.ru/release2.5.1/manual.html
1
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
29 See also here http://bioinf.spbau.ru/en/spades
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
30 </readme>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
31 </package>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
32 </tool_dependency>
0f8b2da62d7d Support for SPAdes 2.5.0. Added a tab-separated output with coverage vs. length info for each contig.
lionelguy
parents:
diff changeset
33