Mercurial > repos > yhoogstrate > package_crossmap_0_2

annotate tool_dependencies.xml @ 3:8ec1bf2ae8a9 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3d756e33e5a551c55cfb91fd95785ce102a8c41f-dirty
author yhoogstrate
date Wed, 26 Aug 2015 10:57:21 -0400
parents 84b0390c3868
children ef54bc5a5347
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="numpy" version="1.9">
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4 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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7 <package name="cython" version="0.20.1">
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8 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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9 </package>
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10
1
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11 <package name="crossmap" version="0.2">
0
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12 <install version="1.0">
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13 <actions>
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14 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
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16 <action type="setup_python_environment">
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17 <repository changeset_revision="749f11b9358a" name="package_cython_0_20_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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18 <package name="cython" version="0.20.1" />
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19 </repository>
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20 <repository changeset_revision="43cb426cb05d" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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21 <package name="numpy" version="1.9" />
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22 </repository>
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23 </action>
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25 <!-- CrossMap doesn't pick up the correct Cython path.
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26 Therefore install it with a manual shell_command instead
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27 of <package></package> inside a pyton_env. -->
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28 <action type="shell_command">
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29 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1(sig_list)/" "bin/CrossMap.py" ;
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30
0
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31 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &amp;&amp;
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33 python setup.py install --root $INSTALL_DIR
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34 </action>
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36 <action type="set_environment">
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37 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
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38 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/dist-packages</environment_variable>
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
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41 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
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42 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
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43 </action>
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44 </actions>
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45 </install>
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46 <readme>
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47 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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48 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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49 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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50 and VCF, reading from remote servers and file compression are supported.
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51
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52 NEWS:
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53 * 08/11/15: Release version 0.2: Fixed the bug that CrossMap will not convert wiggle format files due to name collision with bx python.
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54 * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
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55 - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
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56 the entire file into memory. Users could index their reference genome file using samtools faidx
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57 before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
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58 - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
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59 format.
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60 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
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61 input VCF file contains a INFO field with whitespace.
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62 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
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63 inversions when input file is BED6 or BED12 format.
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64 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
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65 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
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66 as input.
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67 * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
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68 GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
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69 STDOUT to support piping.
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70 * 12/12/13: CrossMap was accepted by Bioinformatics
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71 * 10/23/13: CrossMap (0.1.3) was released
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72
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73 Documentation: http://crossmap.sourceforge.net/
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74 </readme>
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75 </package>
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76 </tool_dependency>