minor: left over from last merge - runs hagfish

lib/python/moa/template/local_templates/autohagfish.jinja2

@@ -0,0 +1,57 @@
+### prepare
+
+if [[ ! -f "db.1.ebwt" ]]
+then
+    echo "Building index for {{ fasta }}"
+    bowtie-build {{ fasta }} db
+else
+    echo "Skip bowtie build - files exists"
+fi
+
+### run
+
+DEBUG=""
+
+mkdir -p touch
+[[ -f "{{ outbase }}.unsorted" ]] || (
+    echo "Running bowtie for"
+    echo "  forward: {{ fw_fq }}"
+    echo "  reverse: {{ rev_fq }}"
+    if [[ $DEBUG == 'echo' ]]
+    then
+        echo bowtie -I 1 -X 10000 -p {{ threads }} --fr  -S \
+            db -1 {{ fw_fq }} -2 {{ rev_fq }}  \
+            \| samtools view -f 2 -bS - \> {{ outbase }}.unsorted
+    else
+        bowtie -I 1 -X 10000 -p {{ threads }} --fr  -S \
+            db -1 {{ fw_fq }} -2 {{ rev_fq }}  \
+            | samtools view -f 2 -bS - > {{ outbase }}.unsorted
+    fi
+)
+
+[[ -f "{{ outbase }}.bam" ]] || (
+    echo "Sorting {{ outbase }}.bam"
+    $DEBUG samtools sort {{ outbase }}.unsorted {{ outbase }}
+)
+
+[[ -f "{{ outbase }}.bai" ]] || (
+    echo "Indexing {{ outbase }}"
+    $DEBUG samtools index {{ outbase }}.bam
+)
+
+[[ -d "readpairs/{{ outbase }}" ]] || (
+    echo "running hagfish_extract for {{ outbase }}"
+    $DEBUG hagfish_extract -v {{ outbase }}.bam 
+)
+
+### finish
+
+hagfish_gapfinder -v -f {{ fasta }}
+hagfish_coverage_combine -v
+hagfish_report -v
+
+### clean
+
+rm -rf `dirname {{ output }}`
+rm -rf bins combined coverage  readpairs  report  seqInfo  stats 
+

lib/python/moa/template/local_templates/autohagfish.moa

@@ -0,0 +1,62 @@
+author: Mark Fiers
+backend: ruff
+commands:
+  run:
+    help: 'Run hagfish'
+    mode: map
+  clean:
+    mode: simple
+    help: remove all Hagfish files
+  finish:
+    help: finish up - find gaps - combine plots - create a report
+    mode: simple
+creation_date: Tue Mar 29 16:34:19 2011
+description: Run the preparatory steps for hagfish
+filesets:
+  fasta:
+    category: prerequisite
+    help: fasta sequence of the reference 
+    type: single
+    optional: false
+  fw_fq:
+    category: input
+    help: 'forward fq input'
+    optional: false
+    pattern: '*/*1.fq'
+    type: set
+  rev_fq:
+    category: input
+    help: 'reverse fq input'
+    optional: true
+    pattern: '*/*2.fq'
+    type: map
+    source: fw_fq
+  outbase:
+    category: output
+    help: 'basename for output files'
+    optional: true
+    pattern: './*'
+    type: map
+    source: fw_fq
+parameters:
+  threads:
+    default: 8
+    help: 'no threads to use'
+    optional: true
+    type: integer
+  min_ok:
+    default: 0
+    help: Minimal acceptable insert size for an aligned pair. If omitted,
+      hagfish will make an estimate
+    optional: true
+    type: int
+  max_ok:
+    default: 0
+    help: Maximal acceptable insert size for an aligned pair. If omitted,
+      hagfish will make an estimate
+    optional: true
+    type: int
+moa_id: autohagfish
+modification_date: Thu, 19 May 2011 20:49:04 +1200
+name: autohagfish
+title: Automatically run bowtie & hagfish combined