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1 =============================================================================
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2 We developed an in-silico method "seq2HLA", written in python and R, which
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3 takes standard paired end RNA-Seq sequence reads in fastq format
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4 as input, uses a bowtie index comprising all HLA alleles and outputs the most
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5 likely HLA class I and class II genotypes, a p-value for each call, and the
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6 expression of each class.
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7 =============================================================================
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8 Author:
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9 Sebastian Boegel
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10 =============================================================================
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11
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12 Tool dependencies:
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13
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14 - bowtie
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15 - R
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16
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17 =============================================================================
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18 To implement this script into Galaxy you have to copy the scripts folder in
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19 your "$GALAXYHOME/tools/" folder and add the path of seq2HLA.xml
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20 to your "$GALAXYHOME/tool_conf.xml"
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21
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22 Example:
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23 # <tool file="rna_seq/mapping_counter.xml" />
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24 # <tool file="rna_seq/count_genes_exons_junctions.xml" />
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25 # <tool file="rna_seq_auto/get_RNA-seq_data.xml" />
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26 # </section>
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27 <section name="HLA Typing" id="hla_type">
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28 <tool file="seq2HLA/seq2HLA.xml"/>
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29 </section>
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30 # <section name="RSeQC" id="rseqc">
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31 # <tool file="RSeQC/bam2wig.xml" />
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32 # <tool file="RSeQC/bam_stat.xml" />
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33 # <tool file="RSeQC/clipping_profile.xml" />
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34 # <tool file="RSeQC/geneBody_coverage.xml" />
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35 # <tool file="RSeQC/infer_experiment.xml" />
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36 ...
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37 ==============================================================================
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38 The script uses in its subprocesses 4 cores, so you will also have to add a
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39 setting to your "$GALAXYHOME/universe_wsgi.ini" to configure the queue for that
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40 script
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41
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42 ...
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43 [galaxy:tool_runners]
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44
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45 #biomart = local:///
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46 #encode_db1 = local:///
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47 #hbvar = local:///
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48 #microbial_import1 = local:///
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49 ucsc_table_direct1 = local:///
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50 #ucsc_table_direct_archaea1 = local:///
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51 #ucsc_table_direct_test1 = local:///
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52 upload1 = local:///
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53 bowtie_wrapper = pbs:////-l nodes=1:ppn=4
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54 bowtie2_wrapper = pbs:////-l nodes=1:ppn=4
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55 tophat = pbs:////-l nodes=1:ppn=4
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56 tophat_color = pbs:////-l nodes=1:ppn=4
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57 cuffdiff = pbs:////-l nodes=1:ppn=4
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58 cufflinks = pbs:////-l nodes=1:ppn=4
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59 cuffmerge = pbs:////-l nodes=1:ppn=4
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60 seqhla = pbs:////-l nodes=1:ppn=6 (this line should be added)
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61 ...
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62 =============================================================================
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