# HG changeset patch
# User yhoogstrate
# Date 1415370749 18000
# Node ID fec34689487160d54e2fc421825222b47336ea68
Uploaded
diff -r 000000000000 -r fec346894871 flaimapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/flaimapper.xml Fri Nov 07 09:32:29 2014 -0500
@@ -0,0 +1,43 @@
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+ Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.
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+ flaimapper
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+ flaimapper
+ -v
+ -f $output_format
+ -o $output
+ -m $mask
+ -r $fasta
+ #for $alignment in $alignments
+ $alignment
+ #end for
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+ FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
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+ doi:10.1093/bioinformatics/btu696
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+
\ No newline at end of file
diff -r 000000000000 -r fec346894871 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Fri Nov 07 09:32:29 2014 -0500
@@ -0,0 +1,8 @@
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+ name, dbkey, value, provider, reference
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\ No newline at end of file
diff -r 000000000000 -r fec346894871 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Nov 07 09:32:29 2014 -0500
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+ git clone --recursive https://github.com/yhoogstrate/flaimapper.git ; git reset --hard "109a7ee13cfad6eb4746422a5382a928e141d0a1" ; cd flaimapper/src ; python setup.py build
+ $INSTALL_DIR/lib/python
+ $INSTALL_DIR/lib64/python
+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python && python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin
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+ $INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python
+ $INSTALL_DIR/bin
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