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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit dc4deb40aeefdf8b20f496626fe0ba28cbe248ed-dirty
author yhoogstrate
date Thu, 12 Nov 2015 15:51:15 -0500
parents 58c2f3e6f23a
children
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="python" version="2.7.10">
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4 <repository changeset_revision="2f32acbaf21a" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
5
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6 <package name="nose" version="1.3.7">
7
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7 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="numpy" version="1.9">
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10 <repository changeset_revision="db045339112b" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="cython" version="0.23.1">
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13 <repository changeset_revision="5212151afa22" name="package_cython_0_23_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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16 <package name="crossmap" version="0.2">
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17 <install version="1.0">
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18 <actions>
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19 <action sha256sum="eb983c8d0ff0331f069e2378768d8988b6b9d8dd303a0f0f0cef9d882256af85" type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.2.tar.gz</action>
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21 <action type="setup_python_environment">
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22 <repository changeset_revision="2f32acbaf21a" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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23 <package name="python" version="2.7.10" />
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24 </repository>
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25 <repository changeset_revision="2e16c2edb44d" name="package_nose_1_3_7" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
5
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26 <package name="nose" version="1.3.7" />
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27 </repository>
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28 <repository changeset_revision="5212151afa22" name="package_cython_0_23_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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29 <package name="cython" version="0.23.1" />
0
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30 </repository>
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31 <repository changeset_revision="db045339112b" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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32 <package name="numpy" version="1.9" />
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33 </repository>
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34 </action>
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35
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36 <!-- If CrossMap is installed with - - home or - - prefix
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37 it often crashes with a 'write-test' error
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39 Using - - root places the installation in:
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40 $INSTALL_DIR / (python path dir) /
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43 The setuptools shipped with galaxy's python version crashes if
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44 a setuptools installation contains a setup_requires tag
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45 -->
0
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46 <action type="shell_command">
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47 sed -i.bak -r "s/numpy.(sum|nan_to_num)+/np.\1/" "bin/CrossMap.py" ;
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48 sed -i.bak -r "s/setup_requires/#setup_requires/" "setup.py" ;
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49
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50 python setup.py install --root $INSTALL_DIR &amp;&amp;
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51 export SUB_DIR=$(dirname $(which python)) &amp;&amp;
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52 mv $INSTALL_DIR$SUB_DIR/../lib $INSTALL_DIR/lib &amp;&amp;
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53 mv $INSTALL_DIR$SUB_DIR $INSTALL_DIR/bin
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54 </action>
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56 <action type="set_environment">
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57 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python2.7/site-packages</environment_variable>
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58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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59
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60 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/bin</environment_variable>
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61 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
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62 </action>
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63 </actions>
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64 </install>
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65 <readme>
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66 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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67 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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68 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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69 and VCF, reading from remote servers and file compression are supported.
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70
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71 NEWS:
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72 * 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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73 * 07/27/15: Release version 0.1.9. For VCF file conversion in v0.1.9:
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74 - CrossMap uses the indexed reference genome (target assembly) sequences rather than load
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75 the entire file into memory. Users could index their reference genome file using samtools faidx
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76 before running CrossMap, otherwise CrossMap will index it automatically the first time you run it.
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77 - In the output VCF file, whether the chromosome IDs contain "chr" or not depends on the input
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78 format.
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79 * 05/15/15: Release version 0.1.8: Fixed the bug that CrossMap will output invalid VCF file when the
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80 input VCF file contains a INFO field with whitespace.
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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81 * 05/04/15: Release version 0.1.7: Address the problem that CrossMap does not convert strand in
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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82 inversions when input file is BED6 or BED12 format.
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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83 * 11/06/14: Release version 0.1.6: Fixed "negative coordinates" bug.
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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84 * 08/05/14: Release version 0.1.5: Support compressed (*.gz, *.Z, *.z, *.bz, *.bz2, *.bzip2) wiggle file
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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85 as input.
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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86 * 05/19/14: add chain files for hg38-&gt;hg19, hg19-&gt;hg38, hg18-&gt;hg38, hg19-&gt;GRCh37,
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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87 GRCh37-&gt;hg19. In CrossMap v0.1.4, conversion results of BAM/SAM files can be directed to
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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88 STDOUT to support piping.
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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89 * 12/12/13: CrossMap was accepted by Bioinformatics
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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90 * 10/23/13: CrossMap (0.1.3) was released
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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91
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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92 Documentation: http://crossmap.sourceforge.net/
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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93 </readme>
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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94 </package>
93b1996b4f7b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 853297e61ca5fecafe4f09ec449e2731515b32c1-dirty
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95 </tool_dependency>