Mercurial > repos > peterjc > clc_assembly_cell
changeset 2:139b6f0a0bb5 draft
v0.0.4 fix recording of clc version
| author | peterjc |
|---|---|
| date | Tue, 01 Sep 2015 06:55:13 -0400 |
| parents | 5ae1c0312aaa |
| children | 9fe1a922353b |
| files | tools/clc_assembly_cell/README.rst tools/clc_assembly_cell/clc_assembler.xml tools/clc_assembly_cell/clc_mapper.xml |
| diffstat | 3 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/tools/clc_assembly_cell/README.rst Wed Aug 05 10:57:39 2015 -0400 +++ b/tools/clc_assembly_cell/README.rst Tue Sep 01 06:55:13 2015 -0400 @@ -88,6 +88,7 @@ v0.0.3 - Reorder XML elements (internal change only). - Added citation tags. - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.0.4 - Bug fix for ``<version_command>`` to capture tool version. ======= ====================================================================== @@ -101,12 +102,12 @@ 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 --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ + $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ ... or:: - $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ + $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/clc_assembly_cell/ ... To just build and check the tar ball, use::
--- a/tools/clc_assembly_cell/clc_assembler.xml Wed Aug 05 10:57:39 2015 -0400 +++ b/tools/clc_assembly_cell/clc_assembler.xml Tue Sep 01 06:55:13 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="clc_assembler" name="CLC assembler" version="0.0.3"> +<tool id="clc_assembler" name="CLC assembler" version="0.0.4"> <description>Assembles reads giving a FASTA file</description> <requirements> <requirement type="binary">clc_assembler</requirement> @@ -8,7 +8,7 @@ <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> - <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> + <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler #for $rg in $read_group ##--------------------------------------
--- a/tools/clc_assembly_cell/clc_mapper.xml Wed Aug 05 10:57:39 2015 -0400 +++ b/tools/clc_assembly_cell/clc_mapper.xml Tue Sep 01 06:55:13 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="clc_mapper" name="CLC Mapper" version="0.0.3"> +<tool id="clc_mapper" name="CLC Mapper" version="0.0.4"> <description>Maps reads giving a SAM/BAM file</description> <requirements> <requirement type="binary">clc_mapper</requirement> @@ -11,7 +11,7 @@ <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> - <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command> + <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper | grep -i version</version_command> <command>echo Mapping reads with clc_mapper... && \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper #for $ref in $references