Mercurial > repos > iuc > package_sra_toolkit_2_5_2

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
author iuc
date Tue, 01 Mar 2016 07:09:32 -0500
parents ab06c0240705
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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
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3 <package name="perl" version="5.18.1">
1
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
iuc
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4 <repository changeset_revision="03f5951a9855" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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5 </package>
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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6 <package name="libmagic" version="5.25">
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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7 <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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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8 </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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9 <package name="ncbi_vdb" version="2.5.2">
1
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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10 <repository changeset_revision="17ae6c0040ea" name="package_ncbi_vdb_2_5_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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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11 </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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12 <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
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13 <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
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14 </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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15 <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
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16 <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
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17 <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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18 <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
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19 <action type="set_environment_for_install">
1
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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20 <repository changeset_revision="03f5951a9855" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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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21 <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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22 </repository>
1
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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23 <repository changeset_revision="21b08f55a6ac" name="package_libmagic_5_25" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
iuc
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24 <package name="libmagic" version="5.25" />
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
iuc
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25 </repository>
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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26 <repository changeset_revision="17ae6c0040ea" name="package_ncbi_vdb_2_5_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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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27 <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
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28 </repository>
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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29 <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
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30 <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
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31 </repository>
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="shell_command">
1
bb51af9130ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit 09fa2b6129e5d156e22b07287b0c3bb61ac41328
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34 ./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=$INSTALL_DIR
0
ab06c0240705 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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35 </action>
ab06c0240705 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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36 <action type="make_install" />
ab06c0240705 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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37 <action type="set_environment">
ab06c0240705 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_sra_toolkit_2_5_2 commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
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38 <environment_variable action="prepend_to" name="PATH">$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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39 </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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40 </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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41 </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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42 <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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43 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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44 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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45 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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46 download of a large SRA data set.
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47
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 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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49 - 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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50 - 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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51 - 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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52 - 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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53 - 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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54 - 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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55 - 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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56
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 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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58
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59 apt-get install build-essential libxml2-dev libcurl4-openssl-dev zlib-dev
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60
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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61 </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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62 </package>
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63 </tool_dependency>