Mercurial > repos > mvdbeek > test_sra

annotate tool_dependencies.xml @ 10:472f8a7e13b3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
author mvdbeek
date Fri, 14 Aug 2015 13:30:47 -0400
parents 9c04607bbb08
children 833f4feaee33
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
1 <?xml version="1.0"?>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
2 <tool_dependency>
2
2c5483e80fb7 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 1
diff changeset
3 <package name="sra_toolkit" version="2.5.2">
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
4 <install version="1.0">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
5 <actions>
9
9c04607bbb08 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 8
diff changeset
6 <!-- <action type="make_directory">src</action>
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
7 <action type="make_directory">build</action>
9
9c04607bbb08 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 8
diff changeset
8 <action type="change_directory">src</action> -->
8
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
9 <action type="download_by_url">https://github.com/ncbi/ncbi-vdb/archive/2.5.2.tar.gz</action>
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
10 <action type="shell_command">
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
11 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
12 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
13 make
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
14 make install
ba27f87d7c36 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 7
diff changeset
15 </action>
5
167041a5893b planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 4
diff changeset
16 <action type="download_by_url">https://github.com/ncbi/ngs/archive/1.1.3.tar.gz</action>
2
2c5483e80fb7 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 1
diff changeset
17 <action type="shell_command">
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
18 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
19 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
20 make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
21 make install
10
472f8a7e13b3 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 9
diff changeset
22 </action>
472f8a7e13b3 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 9
diff changeset
23 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
472f8a7e13b3 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 9
diff changeset
24 <action type="shell_command">
472f8a7e13b3 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 9
diff changeset
25 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build
1
29892b1d24b9 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 0
diff changeset
26 sed -i -e "109s/-static//" tools/copycat/Makefile
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
27 make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
28 make install
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
29 cd $INSTALL_DIR/bin
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
30 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
31 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
32 </action>
10
472f8a7e13b3 planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents: 9
diff changeset
33 <!-- <action type="change_directory">../src</action> -->
0
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
34 <action type="set_environment">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
35 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
36 </action>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
37 </actions>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
38 </install>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
39 <readme>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
40 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
41 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
42 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
43 download of a large SRA data set.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
44
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
45 Build Requirements:
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
46 - make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
47 - git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
48 - gcc
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
49 - g++
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
50 - libxml2
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
51 - libcurl4
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
52 - zlib
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
53
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
54 On a debian based Linux OS use:
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
55
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
56 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
57
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
58 </readme>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
59 </package>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
60 </tool_dependency>