diff README @ 1:155b796033b6 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Dec 21 03:46:15 2012 -0500
@@ -0,0 +1,62 @@
+=============================================================================
+We developed an in-silico method "seq2HLA", written in python and R, which
+takes standard paired end RNA-Seq sequence reads in fastq format
+as input, uses a bowtie index comprising all HLA alleles and outputs the most
+likely HLA class I and class II genotypes, a p-value for each call, and the
+expression of each class.
+=============================================================================
+Author:
+Sebastian Boegel
+=============================================================================
+
+Tool dependencies:
+
+- bowtie
+- R
+
+=============================================================================
+To implement this script into Galaxy you have to copy the scripts folder in
+your "$GALAXYHOME/tools/" folder and add the path of seq2HLA.xml
+to your "$GALAXYHOME/tool_conf.xml"
+
+Example:
+#  <tool file="rna_seq/mapping_counter.xml" />
+#    <tool file="rna_seq/count_genes_exons_junctions.xml" />
+#    <tool file="rna_seq_auto/get_RNA-seq_data.xml" />
+#  </section>
+  <section name="HLA Typing" id="hla_type">
+    <tool file="seq2HLA/seq2HLA.xml"/>
+  </section>
+#  <section name="RSeQC" id="rseqc">
+#    <tool file="RSeQC/bam2wig.xml" />
+#    <tool file="RSeQC/bam_stat.xml" />
+#    <tool file="RSeQC/clipping_profile.xml" />
+#    <tool file="RSeQC/geneBody_coverage.xml" />
+#    <tool file="RSeQC/infer_experiment.xml" />
+...
+==============================================================================
+The script uses in its subprocesses 4 cores, so you will also have to add a
+setting to your "$GALAXYHOME/universe_wsgi.ini" to configure the queue for that
+script
+
+...
+[galaxy:tool_runners]
+
+#biomart = local:///
+#encode_db1 = local:///
+#hbvar = local:///
+#microbial_import1 = local:///
+ucsc_table_direct1 = local:///
+#ucsc_table_direct_archaea1 = local:///
+#ucsc_table_direct_test1 = local:///
+upload1 = local:///
+bowtie_wrapper = pbs:////-l nodes=1:ppn=4
+bowtie2_wrapper = pbs:////-l nodes=1:ppn=4
+tophat = pbs:////-l nodes=1:ppn=4
+tophat_color = pbs:////-l nodes=1:ppn=4
+cuffdiff = pbs:////-l nodes=1:ppn=4
+cufflinks = pbs:////-l nodes=1:ppn=4
+cuffmerge = pbs:////-l nodes=1:ppn=4
+seqhla = pbs:////-l nodes=1:ppn=6               (this line should be added)
+...
+=============================================================================