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sphinx/api/plugin/.gitignore

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+*.rst

sphinx/sync.rst

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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.
+
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sphinx/templates/.gitignore

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+*.rst