Mercurial > repos > mvdbeek > package_sra_tools_2_5_2
comparison tool_dependencies.xml @ 0:ce7da2f8d213 draft
planemo upload commit 96ecd86165525684766848f98a1c3be4353ec3b1-dirty
| author | mvdbeek |
|---|---|
| date | Sat, 15 Aug 2015 09:33:08 -0400 |
| parents | |
| children | da2d93e8fed2 |
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| -1:000000000000 | 0:ce7da2f8d213 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="ncbi_vdb" version="2.5.2"> | |
| 4 <repository changeset_revision="a3f02a928f5e" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="ncbi_ngs" version="1.1.3"> | |
| 7 <repository changeset_revision="f090c319428b" name="package_ngs_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 9 <package name="sra_toolkit" version="2.5.2"> | |
| 10 <install version="1.0"> | |
| 11 <actions> | |
| 12 <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> | |
| 13 <action type="shell_command"> | |
| 14 ./configure --prefix=$INSTALL_DIR --build-prefix=$INSTALL_DIR/build | |
| 15 sed -i -e "109s/-static//" tools/copycat/Makefile | |
| 16 make | |
| 17 make install | |
| 18 cd $INSTALL_DIR/bin | |
| 19 ./vdb-config -s "/repository/user/main/public/cache-enabled=false" | |
| 20 ./vdb-config -s "/repository/user/main/public/root=$INSTALL_DIR" | |
| 21 </action> | |
| 22 <action type="set_environment"> | |
| 23 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 24 </action> | |
| 25 </actions> | |
| 26 </install> | |
| 27 <readme> | |
| 28 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. | |
| 29 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. | |
| 30 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a | |
| 31 download of a large SRA data set. | |
| 32 | |
| 33 Build Requirements: | |
| 34 - make | |
| 35 - git | |
| 36 - gcc | |
| 37 - g++ | |
| 38 - libxml2 | |
| 39 - libcurl4 | |
| 40 - zlib | |
| 41 | |
| 42 On a debian based Linux OS use: | |
| 43 | |
| 44 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev | |
| 45 | |
| 46 </readme> | |
| 47 </package> | |
| 48 </tool_dependency> |