| Previous changeset 6:77cfe958b5ea (2015-09-01) Next changeset 8:4863b1dbe8f0 (2021-04-16) |
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Commit message:
v0.0.10 Internal changes to command line handling |
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modified:
tools/clinod/README.rst tools/clinod/clinod.xml tools/clinod/tool_dependencies.xml |
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| diff -r 77cfe958b5ea -r f61366a4a14e tools/clinod/README.rst --- a/tools/clinod/README.rst Tue Sep 01 06:54:03 2015 -0400 +++ b/tools/clinod/README.rst Tue May 16 08:50:43 2017 -0400 |
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| @@ -73,6 +73,8 @@ v0.0.8 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.0.9 - Explicitly record clinod version via ``<version_command>``. +v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only). + - Single quote command line arguments (internal change only). ======= ====================================================================== @@ -89,17 +91,17 @@ Planemo commands (which requires you have set your Tool Shed access details in ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: - $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/ + $ planemo shed_update -t testtoolshed --check_diff tools/clinod/ ... or:: - $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clinod/ + $ planemo shed_update -t toolshed --check_diff tools/clinod/ ... To just build and check the tar ball, use:: - $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clinod/ + $ planemo shed_upload --tar_only tools/clinod/ ... $ tar -tzf shed_upload.tar.gz test-data/four_human_proteins.fasta |
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| diff -r 77cfe958b5ea -r f61366a4a14e tools/clinod/clinod.xml --- a/tools/clinod/clinod.xml Tue Sep 01 06:54:03 2015 -0400 +++ b/tools/clinod/clinod.xml Tue May 16 08:50:43 2017 -0400 |
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| @@ -1,24 +1,18 @@ -<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.9"> +<tool id="clinod" name="Nucleolar localization sequence Detector (NoD)" version="0.0.10"> <description>Find nucleolar localization signals (NoLSs) in protein sequences</description> <requirements> - <requirement type="binary">java</requirement> <requirement type="package" version="1.3">clinod</requirement> </requirements> - <stdio> - <!-- Assume anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - </stdio> <version_command> ##The first non-blank line contains the version information, e.g. ##NucleOlar localization sequence Detector v. 1.3b (13 May 2011) ##Question: Why don't we have to escape the dollar here? java -jar $CLINOD/clinod-1.3.jar | grep -i "^NucleOlar localization sequence Detector" </version_command> - <command> + <command detect_errors="aggressive"> ##The Galaxy Tool Shed installation should define $CLINOD to point at folder ##containing both clinod-1.3.jar and the batchman binary: -java -jar \$CLINOD/clinod-1.3.jar -in="$fasta_file" -out="$tabular_file" -t="\$GALAXY_SLOTS" -f=MEDIUM_TAB -nonols -clean_sequence +java -jar \$CLINOD/clinod-1.3.jar -in='$fasta_file' -out='$tabular_file' -t="\${GALAXY_SLOTS:-4}" -f=MEDIUM_TAB -nonols -clean_sequence ##TODO - Make the -clean_sequence argument a parameter? </command> <inputs> |
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| diff -r 77cfe958b5ea -r f61366a4a14e tools/clinod/tool_dependencies.xml --- a/tools/clinod/tool_dependencies.xml Tue Sep 01 06:54:03 2015 -0400 +++ b/tools/clinod/tool_dependencies.xml Tue May 16 08:50:43 2017 -0400 |
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| @@ -2,21 +2,34 @@ <tool_dependency> <package name="clinod" version="1.3"> <install version="1.0"> - <actions> + <actions_group> + <!-- Download the JAR, and SNNS binary for 64bit Linux --> + <actions os="linux" architecture="x86_64"> + <!-- Main JAR file --> + <!-- Original URL http://www.compbio.dundee.ac.uk/www-nod/downloads/clinod-1.3.jar --> + <action type="download_file" sha256sum="45d80662ba109a7af28aeafcfb2ca417a7d575ac3700f69bd40965a69d41e072" target_filename="clinod-1.3.jar">https://depot.galaxyproject.org/software/clinod/clinod_1.3_src_all.jar</action> + <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR/</destination></action> + <!-- clinod requires the SNNS Batch Interpreter v1.0 executable --> + <!-- Original URL http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz --> + <action type="download_file" sha256sum="54bf92d23e9198f9030a3c3d2b741472e9b8660b27d3b419ade6393b1ebf6f62" target_filename="SNNSv4.3.tar.gz">https://depot.galaxyproject.org/software/SNNS/SNNS_4.3_linux_x64.tar.gz</action> + <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action> + <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action> + </actions> + <actions> + <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action> + <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action> + <action type="shell_command">uname</action> + <action type="shell_command">arch</action> + <action type="shell_command">echo "Please report this via https://github.com/peterjc/pico_galaxy/issues - thank you!"</action> + <action type="shell_command">false</action> + <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install --> + </actions> + <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> <!-- Set environment variable $CLINOD so wrapper knows where to look --> <action type="set_environment"> - <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="CLINOD" action="set_to">$INSTALL_DIR/</environment_variable> </action> - <!-- clinod requires the SNNS Batch Interpreter v1.0 executable --> - <action type="shell_command">wget http://www.ra.cs.uni-tuebingen.de/downloads/SNNS/SNNSv4.3.tar.gz</action> - <action type="shell_command">tar -zxvf SNNSv4.3.tar.gz</action> - <action type="move_file"><source>SNNSv4.3/tools/bin/x86_64-pc-unknown-linux-gnuoldld/batchman</source><destination>$INSTALL_DIR/</destination></action> - <!-- clinod itself is just a JAR file --> - <action type="shell_command">wget http://www.compbio.dundee.ac.uk/nod/downloads/clinod-1.3.jar</action> - <!-- Don't need to move it, $INSTALL_DIR is the current directory - <action type="move_file"><source>clinod-1.3.jar</source><destination>$INSTALL_DIR</destination></action> - --> - </actions> + </actions_group> </install> <readme> Downloads and installs the command line NoD (clinod) JAR file and the binary @@ -31,4 +44,3 @@ </readme> </package> </tool_dependency> - |