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comparison tools/clinod/README.rst @ 8:4863b1dbe8f0 draft

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"Update all the pico_galaxy tools on main Tool Shed"
author peterjc
date Fri, 16 Apr 2021 22:33:30 +0000
parents f61366a4a14e
children b6ea129299ea
comparison
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7:f61366a4a14e 8:4863b1dbe8f0
21 Neural Network Simulator (SNNS), and set the ``$CLINOD`` to their folder. 21 Neural Network Simulator (SNNS), and set the ``$CLINOD`` to their folder.
22 22
23 23
24 Manual Installation 24 Manual Installation
25 =================== 25 ===================
26 This wrapper expects the java binary to be on the system PATH, and to be able 26 This wrapper expects the java binary to availabe via a wapper script named
27 to access command line NoD as ``$CLINOD/clinod-1.3.jar`` which means if you 27 ``clinod`` on the system ``$PATH``.
28 used ``/opt/clinod/clinod-1.3.jar`` set the environment variable ``$CLINOD`` 28
29 to ``/opt/clinod`` 29 Older versions of this tool called the JAR file directly via an environment
30 variable as ``$CLINOD/clinod-1.3.jar`` - this is no longer used.
30 31
31 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network 32 Internally NoD calls the binary batchman v1.0 from the Stuttgart Neural Network
32 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the 33 Simulator (SNNS) v4.2 or 4.3 software suite. This binary can either be on the
33 system path or located next to the JAR file, i.e. ``/opt/clinod/batchman`` 34 system path or located next to the JAR file, i.e. ``/opt/clinod/batchman``
34 35
73 v0.0.8 - Reorder XML elements (internal change only). 74 v0.0.8 - Reorder XML elements (internal change only).
74 - Planemo for Tool Shed upload (``.shed.yml``, internal change only). 75 - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
75 v0.0.9 - Explicitly record clinod version via ``<version_command>``. 76 v0.0.9 - Explicitly record clinod version via ``<version_command>``.
76 v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only). 77 v0.0.10 - Use ``<command detect_errors="aggressive">`` (internal change only).
77 - Single quote command line arguments (internal change only). 78 - Single quote command line arguments (internal change only).
79 v0.1.0 - Calls the JAR file via a wrapper script ``clinod``, in order to use
80 the BioConda package OR the ``tool_dependencies.xml`` system.
81 To do this the Tool Shed XML installation recipe now installs the
82 same wrapper script ``clinod`` used in the BioConda package for
83 calling the JAR file.
78 ======= ====================================================================== 84 ======= ======================================================================
79 85
80 86
81 Developers 87 Developers
82 ========== 88 ==========
101 107
102 To just build and check the tar ball, use:: 108 To just build and check the tar ball, use::
103 109
104 $ planemo shed_upload --tar_only tools/clinod/ 110 $ planemo shed_upload --tar_only tools/clinod/
105 ... 111 ...
106 $ tar -tzf shed_upload.tar.gz 112 $ tar -tzf shed_upload.tar.gz
107 test-data/four_human_proteins.fasta 113 test-data/four_human_proteins.fasta
108 test-data/four_human_proteins.clinod-1.3.tabular 114 test-data/four_human_proteins.clinod-1.3.tabular
109 tools/clinod/README.rst 115 tools/clinod/README.rst
110 tools/clinod/clinod.xml 116 tools/clinod/clinod.xml
111 tools/clinod/tool_dependencies.xml 117 tools/clinod/tool_dependencies.xml