Mercurial > repos > iuc > package_sra_toolkit_2_5_2
annotate tool_dependencies.xml @ 0:ab06c0240705 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author | iuc |
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date | Sun, 06 Dec 2015 09:04:27 -0500 |
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children | bb51af9130ea |
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ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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1 <?xml version="1.0"?> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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2 <tool_dependency> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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3 <package name="perl" version="5.18.1"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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4 <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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5 </package> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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6 <package name="ncbi_vdb" version="2.5.2"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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7 <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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8 </package> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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9 <package name="ngs_sdk" version="1.1.3"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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10 <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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11 </package> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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12 <package name="sra_toolkit" version="2.5.2"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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13 <install version="1.0"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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14 <actions> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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15 <action type="download_by_url">https://github.com/ncbi/sra-tools/archive/2.5.2.tar.gz</action> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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16 <action type="set_environment_for_install"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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17 <repository changeset_revision="8b3509930a44" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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18 <package name="perl" version="5.18.1" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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19 </repository> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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20 <repository changeset_revision="b980182ad267" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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21 <package name="ncbi_vdb" version="2.5.2" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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22 </repository> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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23 <repository changeset_revision="1197d3c98375" name="package_ngs_sdk_1_1_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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24 <package name="ngs_sdk" version="1.1.3" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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25 </repository> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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26 </action> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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27 <action type="shell_command"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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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=$INSTALL_DIR/build |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
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29 </action> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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30 <action type="shell_command"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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31 sed -i -e "109s/-static//" tools/copycat/Makefile |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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32 </action> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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33 <action type="make_install" /> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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34 <action type="set_environment"> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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35 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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36 </action> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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37 </actions> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 </install> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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39 <readme> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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40 Tools from NCBI SRA Toolkit for extracting FASTQ and SAM format reads from SRA format archives. |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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41 This software release was designed to run under Linux, MacOSX operating systems on Intel x86-compatible 64 bit architectures. |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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42 When running on Amazon EC2, be sure to keep in mind the size limitation of EBS storage devices when requesting a |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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43 download of a large SRA data set. |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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44 |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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45 Build Requirements: |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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46 - make |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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47 - git |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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48 - gcc |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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49 - g++ |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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50 - libxml2 |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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51 - libcurl4 |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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52 - zlib |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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53 |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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54 On a debian based Linux OS use: |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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55 |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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56 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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57 |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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58 </readme> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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59 </package> |
ab06c0240705
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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60 </tool_dependency> |