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comparison tools/clc_assembly_cell/README.rst @ 5:31a9169b6222 draft default tip

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"Update all the pico_galaxy tools on main Tool Shed"
author peterjc
date Fri, 16 Apr 2021 22:32:53 +0000
parents 46a667b5e19e
children
comparison
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4:46a667b5e19e 5:31a9169b6222
93 unmapped reads in the CLC Mapper wrapper. 93 unmapped reads in the CLC Mapper wrapper.
94 - Bug fix to use the ``$CLC_ASSEMBLY_CELL`` environment variable when 94 - Bug fix to use the ``$CLC_ASSEMBLY_CELL`` environment variable when
95 calling ``clc_cas_to_sam`` in the CLC MApper wrapper. 95 calling ``clc_cas_to_sam`` in the CLC MApper wrapper.
96 v0.0.6 - Update tool XML for optional vs required parameters. 96 v0.0.6 - Update tool XML for optional vs required parameters.
97 - Update URLs in documentation. 97 - Update URLs in documentation.
98 v0.0.7 - Use ``<command detect_errors="aggressive">`` (internal change only).
99 - Single quote command line arguments (internal change only).
98 ======= ====================================================================== 100 ======= ======================================================================
99 101
100 102
101 Developers 103 Developers
102 ========== 104 ==========
106 108
107 For pushing a release to the test or main "Galaxy Tool Shed", use the following 109 For pushing a release to the test or main "Galaxy Tool Shed", use the following
108 Planemo commands (which requires you have set your Tool Shed access details in 110 Planemo commands (which requires you have set your Tool Shed access details in
109 ``~/.planemo.yml`` and that you have access rights on the Tool Shed):: 111 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
110 112
111 $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ 113 $ planemo shed_update -t testtoolshed --check_diff tools/clc_assembly_cell/
112 ... 114 ...
113 115
114 or:: 116 or::
115 117
116 $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ 118 $ planemo shed_update -t toolshed --check_diff tools/clc_assembly_cell/
117 ... 119 ...
118 120
119 To just build and check the tar ball, use:: 121 To just build and check the tar ball, use::
120 122
121 $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/clc_assembly_cell/ 123 $ planemo shed_upload --tar_only tools/clc_assembly_cell/
122 ... 124 ...
123 $ tar -tzf shed_upload.tar.gz 125 $ tar -tzf shed_upload.tar.gz
124 test-data/NC_010642.fna 126 test-data/NC_010642.fna
125 tools/clc_assembly_cell/README.rst 127 tools/clc_assembly_cell/README.rst
126 tools/clc_assembly_cell/clc_assembler.xml 128 tools/clc_assembly_cell/clc_assembler.xml