ongoing work on docs

_sources/api/plugin/checkversion.txt

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+.. automodule:: moa.plugin.checkversion
+   :members:

_sources/api/plugin/doc.txt

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+.. automodule:: moa.plugin.doc
+   :members:

_sources/api/plugin/mail.txt

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+.. automodule:: moa.plugin.mail
+   :members:

_sources/api/plugin/metavar.txt

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+.. automodule:: moa.plugin.metavar
+   :members:

_sources/api/plugin/project.txt

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+.. automodule:: moa.plugin.project
+   :members:

_sources/api/plugin/report.txt

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+.. automodule:: moa.plugin.report
+   :members:

_sources/api/plugin/sgeActor.txt

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+.. automodule:: moa.plugin.sgeActor
+   :members:

_sources/api/plugin/umask.txt

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+.. automodule:: moa.plugin.umask
+   :members:

_sources/api/plugin/varInject.txt

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+.. automodule:: moa.plugin.varInject
+   :members:

_sources/sync.txt

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+Synchronizing jobs
+==================
+
+It is quite often usefull to repeat a jobs on a number of different
+input files. For simple operations, one liners, this ca be
+accomplished using `moa map`. More complex operations, or those
+requiring a template other than `map` can be replicated using job
+syncronization. Assume you have a set of fastq libraries, each in it's
+own directory::
+
+    ./fq/set1/set1_1.fq
+    ./fq/set1/set1_2.fq
+    ./fq/set2/set2_1.fq
+    ./fq/set2/set2_2.fq
+    ./fq/set3/set3_1.fq
+    ./fq/set3/set3_2.fq
+
+And you want to run a bowtie alignment for each separately. The
+approach to take is to create a directory containing all alignments::
+
+
+    mkdir bowtie
+    cd bowtie
+
+and, in that directory, create one job running bowtie, in a directory
+named **exactly** as the input directories::
+
+    mkdir set1
+    cd set1
+    moa new bowtie -t 'run bowtie for {{_}}'
+
+Note the magic variable `{{_}}`. This variable is replaced by the name
+of the current directory. So when running `moa show`, the title would
+show up as "run bowtie for set1". This magic variable can be used in
+all variables, and we'll use it here to set this job up in such a way
+that it can be reused for the other datasets::
+
+   set moa fq_forward_input='../../fq/{{_}}/*_1.fq'
+   # .. configure the remaining variables
+
+Now - we replicate this directory in the following manner. We'll move
+one directory up, to the `bowtie` directory, and create a `sync` job::
+
+    cd ..
+    moa new sync -t 'run bowtie for all fq datasets'
+    moa set source=../fq/
+
+The sync template keeps directories synchronized, based on the
+`source` directory. If you now run `moa run` in the `bowtie`
+directory, two more directories will be created: `set2` and `set3`,
+each containing a verbatim copy of the original bowtie job created. 
+
+If, at a certain moment you obtain more fastq datasets::
+
+    ./fq/set4/set4_1.fq
+    ./fq/set4/set4_2.fq
+
+you can repeat `moa run` in the `./bowtie` sync directory, and a new
+directory will be created. Note that the `sync` template will not
+remove directories. Also if you want to update the configuration of
+the syncronized bowtie jobs, you only need to change the configuration
+in one directory, run `moa run` again in the `./bowtie` directory and
+the configuration is synchronized across all jobs.
+
+
+
+
+
+
+
+
+
+
+
+

_sources/templates/archroot.txt

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+archroot
+------------------------------------------------
+
+**Helper script for a root archive**
+
+
+    Helper script for the root of an archive template
+
+
+
+Commands
+~~~~~~~~
+
+**run**
+  *no help defined*
+
+
+
+Parameters
+~~~~~~~~~~
+
+
+
+**moa_archive_parameters**
+  space separated list of parameters to set for this template
+
+  | *type*: `string`
+  | *default*: `{}`
+  | *optional*: `False`
+
+
+
+miscellaneous
+~~~~~~~~~~~~~
+
+**Backend**
+  ruff
+**Author**
+  Mark Fiers
+**Creation date**
+  Tue, 17 Apr 2012 10:21:31
+**Modification date**
+  Tue, 17 Apr 2012 10:21:25

_sources/templates/filterwgs_pair.txt

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+filterwgs_pair
+------------------------------------------------
+
+**Execute a "map22" ad-hoc analysis - two input files, two output files**
+
+
+    Filter raw WGS data
+
+
+
+Commands
+~~~~~~~~
+
+**run**
+  Filter WGS data
+
+
+
+Filesets
+~~~~~~~~
+
+
+**input1**
+  forward input fastq
+
+
+
+
+
+**input2**
+  reverse input fastq
+
+
+  | *type*: `map`
+  | *source*: `input1`
+  | *category*: `input`
+  | *optional*: `False`
+  | *pattern*: `*/*`
+
+
+
+
+**output1**
+  forward output fastq
+
+
+  | *type*: `map`
+  | *source*: `input1`
+  | *category*: `output`
+  | *optional*: `True`
+  | *pattern*: `./*`
+
+
+
+
+**output2**
+  reverse output fastq
+
+
+  | *type*: `map`
+  | *source*: `input1`
+  | *category*: `output`
+  | *optional*: `True`
+  | *pattern*: `./*`
+
+
+
+
+
+Parameters
+~~~~~~~~~~
+
+
+
+**adapters**
+  Fasta file with the adapter sequences to trim
+
+  | *type*: `file`
+  | *default*: `{}`
+  | *optional*: `False`
+
+
+
+**minlen**
+  Minimum remaining sequence length
+
+  | *type*: `int`
+  | *default*: `50`
+  | *optional*: `True`
+
+
+
+**qual**
+  quality threshold causing trimming
+
+  | *type*: `int`
+  | *default*: `13`
+  | *optional*: `True`
+
+
+
+**title**
+
+
+  | *type*: `{}`
+  | *default*: `Filter paired fastq files using fastq-mcf`
+  | *optional*: `{}`
+
+
+
+miscellaneous
+~~~~~~~~~~~~~
+
+**Backend**
+  ruff
+**Author**
+  Mark Fiers
+**Creation date**
+  Tue Mar 29 16:34:19 2011
+**Modification date**
+  Mon, 13 Feb 2012 09:16:36 +1300

_sources/templates/map2.txt

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+map2
+------------------------------------------------
+
+**Execute a "map2" ad-hoc analysis**
+
+
+    Execute one command, on a number of input files.
+
+
+
+Commands
+~~~~~~~~
+
+**run**
+  *no help defined*
+
+
+
+Filesets
+~~~~~~~~
+
+
+**input1**
+  "map" input files set 1
+
+
+
+
+
+**input2**
+  "map" input files set 2
+
+
+  | *type*: `map`
+  | *source*: `input1`
+  | *category*: `input`
+  | *optional*: `False`
+  | *pattern*: `*/*`
+
+
+
+
+**output**
+  "map" output files
+
+
+  | *type*: `map`
+  | *source*: `input1`
+  | *category*: `output`
+  | *optional*: `True`
+  | *pattern*: `./*`
+
+
+
+
+
+Parameters
+~~~~~~~~~~
+
+
+
+**process**
+  The command to execute
+
+  | *type*: `string`
+  | *default*: `True`
+  | *optional*: `False`
+
+
+
+miscellaneous
+~~~~~~~~~~~~~
+
+**Backend**
+  ruff
+**Author**
+  Mark Fiers
+**Creation date**
+  Tue Mar 29 16:34:19 2011
+**Modification date**
+  Wed Mar 30 06:02:01 2011