Mercurial > repos > mvdbeek > test_sra

annotate tool_dependencies.xml @ 0:ec8b334b5ebb 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 12:23:28 -0400
parents
children 29892b1d24b9
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>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
3 <package name="sra_toolkit" version="2.4.5">
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>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
6 <action type="make_directory">src</action>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
7 <action type="make_directory">build</action>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
8 <action type="change_directory">src</action>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
9 <action type="shell_command">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
10 git clone https://github.com/mdshw5/sra-tools.git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
11 git clone https://github.com/mdshw5/ncbi-vdb.git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
12 git clone https://github.com/mdshw5/ngs.git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
13 LD_LIBRARY_PATH=LD_LIBRARY_PATH:$INSTALL_DIR/lib64:$INSTALL_DIR/lib
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
14 cd $INSTALL_DIR/src/ncbi-vdb
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
15 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
16 make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
17 make install
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
18 cd $INSTALL_DIR/src/ngs/ngs-sdk
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
19 ./configure --prefix=$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
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
22 cd $INSTALL_DIR/src/sra-tools
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
23 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build --with-ncbi-vdb-build=$INSTALL_DIR/build --with-ncbi-vdb-sources=$INSTALL_DIR/src/ncbi-vdb --with-ngs-sdk-prefix=$INSTALL_DIR
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
24 sed -i -e "109s///" tools/copycat/Makefile
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
25 make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
26 make install
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
27 cd $INSTALL_DIR/bin
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
28 ./vdb-config -s "/repository/user/main/public/cache-enabled=false"
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
29 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR"
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
30 </action>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
31 <action type="set_environment">
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
32 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
33 </action>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
34 </actions>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
35 </install>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
36 <readme>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
37 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
38 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
39 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
40 download of a large SRA data set.
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
41
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
42 Build Requirements:
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
43 - make
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
44 - git
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
45 - gcc
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
46 - g++
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
47 - libxml2
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
48 - libcurl4
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
49 - zlib
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
50
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
51 On a debian based Linux OS use:
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
52
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
53 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
54
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
55 </readme>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
56 </package>
ec8b334b5ebb planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
mvdbeek
parents:
diff changeset
57 </tool_dependency>