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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/packages/package_sra_toolkit_2_5_2 commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
author mvdbeek
date Wed, 04 Nov 2015 07:09:56 -0500
parents 88273fd00182
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="ascp" version="3">
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4 <repository changeset_revision="e109f0ec22c3" name="package_ascp_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="perl" version="5.18.1">
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7 <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="ncbi_vdb" version="2.5.2">
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10 <repository changeset_revision="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="ngs_sdk" version="1.1.3">
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13 <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="sra_toolkit" version="2.5.2">
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16 <install version="1.0">
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17 <actions>
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18 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action>
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19 <action type="set_environment_for_install">
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20 <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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21 <package name="perl" version="5.18.1" />
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22 </repository>
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23 <repository changeset_revision="1d307129f4f2" name="package_ncbi_vdb_2_5_2" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu">
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24 <package name="ncbi_vdb" version="2.5.2" />
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25 </repository>
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26 <repository changeset_revision="2cc3f1941cb5" name="package_ngs_sdk_1_1_3" owner="mvdbeek" toolshed="https://toolshed.g2.bx.psu.edu">
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27 <package name="ngs_sdk" version="1.1.3" />
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28 </repository>
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29 </action>
1
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30 <action type="shell_command">
0
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31 ./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=$INSTALL_DIR/build
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32 </action>
1
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33 <action type="shell_command">
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34 sed -i -e "109s/-static//" tools/copycat/Makefile ; make ; make install
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35 </action>
0
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36 <action type="set_environment">
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37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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38 </action>
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39 </actions>
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40 </install>
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41 <readme>
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42 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives.
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43 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures.
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44 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a
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45 download of a large SRA data set.
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46
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47 Build Requirements:
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48 - make
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49 - git
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50 - gcc
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51 - g++
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52 - libxml2
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53 - libcurl4
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54 - zlib
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55
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56 On a debian based Linux OS use:
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57
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58 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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59
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60 </readme>
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61 </package>
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62 </tool_dependency>