Mercurial > repos > iuc > package_sra_toolkit_2_5_2
annotate tool_dependencies.xml @ 1:2255f3e3cbb3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
| author | iuc |
|---|---|
| date | Tue, 22 Dec 2015 19:41:24 -0500 |
| parents | 91924fa830bb |
| children | 163cf5b7c14e |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="perl" version="5.18.1"> | |
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2255f3e3cbb3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
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0
diff
changeset
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4 <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 6 <package name="ncbi_vdb" version="2.5.2"> | |
| 7 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 9 <package name="ngs_sdk" version="1.1.3"> | |
| 10 <repository changeset_revision="1381744a8a09" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 11 </package> | |
| 12 <package name="sra_toolkit" version="2.5.2"> | |
| 13 <install version="1.0"> | |
| 14 <actions> | |
| 15 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> | |
| 16 <action type="set_environment_for_install"> | |
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2255f3e3cbb3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit bd736b6361ba659a1251dd1a1a05f7e3b633bdf5
iuc
parents:
0
diff
changeset
|
17 <repository changeset_revision="d5193a5f6203" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> |
| 0 | 18 <package name="perl" version="5.18.1" /> |
| 19 </repository> | |
| 20 <repository changeset_revision="b0638a3ba7e6" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 21 <package name="ncbi_vdb" version="2.5.2" /> | |
| 22 </repository> | |
| 23 <repository changeset_revision="1381744a8a09" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 24 <package name="ngs_sdk" version="1.1.3" /> | |
| 25 </repository> | |
| 26 </action> | |
| 27 <action type="shell_command"> | |
| 28 ./configure --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=$INSTALL_DIR/build | |
| 29 </action> | |
| 30 <action type="shell_command"> | |
| 31 sed -i -e "109s/-static//" tools/copycat/Makefile | |
| 32 </action> | |
| 33 <action type="make_install" /> | |
| 34 <action type="set_environment"> | |
| 35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 36 </action> | |
| 37 </actions> | |
| 38 </install> | |
| 39 <readme> | |
| 40 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. | |
| 41 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. | |
| 42 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a | |
| 43 download of a large SRA data set. | |
| 44 | |
| 45 Build Requirements: | |
| 46 - make | |
| 47 - git | |
| 48 - gcc | |
| 49 - g++ | |
| 50 - libxml2 | |
| 51 - libcurl4 | |
| 52 - zlib | |
| 53 | |
| 54 On a debian based Linux OS use: | |
| 55 | |
| 56 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev | |
| 57 | |
| 58 </readme> | |
| 59 </package> | |
| 60 </tool_dependency> |