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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="507f3ab4e38d" 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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5 </package>
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6
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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
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11 <package name="crossmap" version="0.1.8">
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12 <install version="1.0">
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13 <actions>
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14 <action type="download_by_url">http://sourceforge.net/projects/crossmap/files/CrossMap-0.1.8.tar.gz</action>
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15
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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="507f3ab4e38d" name="package_python_2_7_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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8
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23 </action>
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24
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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 the pyton_env. -->
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28 <action type="shell_command">
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29 export PYTHONPATH="$CYTHON_PATH/lib/python/Cython-0.20.1-py2.7-linux-x86_64.egg:$PYTHONPATH" &&
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30
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31 export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &&
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32 python setup.py install --install-dir $INSTALL_DIR --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
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33 </action>
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3
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34
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35 <action type="set_environment">
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36 <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/usr/local/lib/python2.7/site-packages</environment_variable>
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37 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/usr/local/bin</environment_variable>
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38
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39 <environment_variable action="set_to" name="PATH_CROSSMAP">$INSTALL_DIR/usr/local/bin</environment_variable>
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40 <environment_variable action="set_to" name="CROSSMAP_ROOT_DIR">$INSTALL_DIR</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>
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45 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
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46 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
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47 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
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48 and VCF, reading from remote servers and file compression are supported.
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49
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50 Installation
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51
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52 Prerequisite:
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53 * gcc
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54 * python2.7 or newer
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55 * numpy
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56 * cython
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57
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58 Download CrossMap program from here:
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59
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60 $ tar zxf CrossMap-VERSION.tar.gz
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61
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62 $ cd CrossMap-VERSION
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63
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64 # install CrossMap to default location. In Linux/Unix, this location is like:
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65 # /home/user/lib/python2.7/site-packages/
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66 $ python setup.py install
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67
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68 # or you can install CrossMap to a specified location:
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69 $ python setup.py install --root=/home/user/CrossMap
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70
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71 # setup PYTHONPATH. Skip this step if CrossMap was installed to default location.
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72 $ export PYTHONPATH=/home/user/CrossMap/usr/local/lib/python2.7/site-packages:$PYTHONPATH.
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73
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74 # Skip this step if CrossMap was installed to default location.
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75 $ export PATH=/home/user/CrossMap/usr/local/bin:$PATH
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76
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77 NOTE:
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78
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79 * Due to intensive computation, CrossMap is designed to run on Linux/Unix and Mac OS. Some modules may not work properly on Windows.
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80 * Mac users need to download and install Xcode command line tools.
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81
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82 Documentation: http://crossmap.sourceforge.net/
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83 </readme>
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84 </package>
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85 </tool_dependency>
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