Unix Command lien tool wrappers for Galaxy ========================================== This package contains XML definition files for the Galaxy framework (http://main.g2.bx.psu.edu/). These tools extend the already existing text processing tools in Galaxy. Available Tools =============== Simple Text Processing: find & replace text in line find & replace text in a specific column remove ending of a file GNU core utils: awk sek grep (with or without highlighted output) cut sort uniq join Requirements ============ COREUTILS-7.1 ------------- The to run the tools, you'll need GNU coreutils package version 7.1 or later. See http://www.gnu.org/software/coreutils/ Example: $ wget http://ftp.gnu.org/gnu/coreutils/coreutils-7.1.tar.gz $ tar -xzvf coreutils-7.1.tar.gz $ cd coreutils-7.1 $ ./configure $ make $ sudo make install AWK --- To run AWK safely, you'll need support for the 'sandbox' feature. Currently ( March 2009 ), the 'sandbox' feature is available only in the development branch of AWK. Example: $ cvs -d:pserver:anonymous@cvs.sv.gnu.org:/sources/gawk co gawk-devel $ cd gawk-devel $ ./configure $ make $ sudo make install SED --- To run SED safely, you'll need support for the 'sandbox' feature. Currently ( March 2009 ), you'll need to manually patch a recent version of SED to add the 'sandbox' feature. The patch is found in the 'patches' sub-directory. Example: $ wget http://ftp.gnu.org/gnu/sed/sed-4.1.5.tar.gz $ tar -xvzf sed-4.1.5.tar.gz $ cd sed-4.1.5 $ patch -p 1 < [PATH]/sed-4.1.5-sandbox.patch $ ./configure $ make $ sudo make install Galaxy Installation =================== You'll need a local Galaxy installation to use these tools. run: $ ./install_galaxy_files.sh [GALAXY-SERVER-DIRECTORY] to copy the needed files to the Galaxy root. Under /tools a new directory named 'unix_tools' will be created. In /test-data some files will be placed (for the functional testing). Now, manually merge the content of 'tool_conf.xml.add' into your Galaxy's tool_conf.xml file. Functional Testing ================== Some of the unix tools have a functional unit-test files. To run the functional testing in Galaxy, add the content of 'tool_conf.xml.add' to your Galaxy's tool_conf.xml.sample (NOTE: not tool_conf.xml, but tool_conf.xml.sample). Then, from Galaxy's root directory, run: $ sh run_functional_tests.sh -id cshl_awk_tool $ sh run_functional_tests.sh -id cshl_sed_tool $ sh run_functional_tests.sh -id cshl_grep_tool $ sh run_functional_tests.sh -id cshl_sort_tool $ sh run_functional_tests.sh -id cshl_cut_tool $ sh run_functional_tests.sh -id Remove_ending $ sh run_functional_tests.sh -id cshl_sed_replace_in_line $ sh run_functional_tests.sh -id cshl_awk_replace_in_column If the results of the tests is anyhthing other than "OK", you'll need to fix whatever is wrong. If the AWK tool failed, make sure you've installed AWK with the 'sandbox' patch. If the SED tool failed, make sure you've installed SED with the 'sandbox' patch. If the sort tool failed, make sure you've installed coreutils version 7.1 or later. LICENSE ============ All files in this package are released under the same license as Galaxy (http://g2.trac.bx.psu.edu/browser/LICENSE.txt) CONTACT ======= Send suggestions, comments, and bug reports to: gordon cshl.edu