Mercurial > repos > sebastian-boegel > seq2hla
diff README @ 1:155b796033b6 draft default tip
Uploaded
author | sebastian-boegel |
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date | Fri, 21 Dec 2012 03:46:15 -0500 |
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--- /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) +... +=============================================================================