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isoem2_isode2/README.txt isoem2_isode2/isoem_wrapper.xml isoem2_isode2/tool_data_table_conf.xml isoem2_isode2/tool_data_table_conf.xml.sample |
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| diff -r be08c88b353e -r cff0a5f324d4 isoem2_isode2/README.txt --- a/isoem2_isode2/README.txt Sun Mar 26 22:27:30 2017 -0400 +++ b/isoem2_isode2/README.txt Sat Apr 01 10:59:38 2017 -0400 |
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| @@ -1,11 +1,24 @@ To install IsoEM2, IsoDE2 and the FC filter 1) Follow Galaxy instructions for installing a tool from the Tool Shed + 2) Download and install IsoEM2/IsoDE2 (https://github.com/mandricigor/isoem2) + 3) Install other dependencies: - tmap (needed for ION Torrent data) -- hisat2 (needed for Illumina data) -- prinseq -- bedtools + Available at https://github.com/iontorrent/TMAP +- hisat2 (needed for Illumina data) + Available at https://ccb.jhu.edu/software/hisat2/index.shtml +- prinseq + Available at http://prinseq.sourceforge.net/ +- bedtools available at + http://bedtools.readthedocs.io/en/latest/ + 4) Edit isoem_wrapper.sh and IsoDE2.sh. Change tool paths to where they are installed on your system - + +5) build hisat2 and/or tmap index, depending on the type of your RNA-Seq data, for the reference you will use for mapping + +6) Edit the .loc file with paths to your reference files: GTF, Transcript to gene cluster, and mapper indices), and copy it under tool-data directory in Galaxy +Note: If you need only one of the two mappers (say hisat2), you can replace the other path to the other maaper index with a dummy path + +7) copy the entry in the tool_data_table_conf.xml file provided in this repository to the tool_data_table_conf.xml in your Galaxy config directory |
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| diff -r be08c88b353e -r cff0a5f324d4 isoem2_isode2/isoem_wrapper.xml --- a/isoem2_isode2/isoem_wrapper.xml Sun Mar 26 22:27:30 2017 -0400 +++ b/isoem2_isode2/isoem_wrapper.xml Sat Apr 01 10:59:38 2017 -0400 |
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| @@ -40,7 +40,7 @@ </command> <inputs> - <param name="sampleName" size="10" type="text" label="Sample name" value="Sample1"/> + <param name="sampleName" size="10" type="text" label="Sample name" value="Sample" help="Output files label"/> <conditional name="referenceSource"> <param name="CCDSsource" type="select" label="Will you upload a reference transcriptome fasta file from your history or use a built-in reference?" help="Built-ins were indexed using default options"> @@ -127,45 +127,10 @@ ----- - -**BUILT-IN REFERENCES** - -**mm10_C57BL/6:** - -* GTF file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna.GTF -* TMAP_index:/import1/tmap-index/tmap3.4.1/mm10/CCDS_nucleotide.20140407.fna -* HISAT2_index: /import1/hisat2-index/mm10_CCDS/mm10_CCDS_nucleotide.20140407 -* Cluster file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna_transcriptID_geneName.txt - -**mm10_BALB/c:** - -* GTF file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna.GTF -* TMAP_index: /import1/tmap-index/tmap3.4.1/mm10/mm10_CCDS_nucleotide.20140407_BALBc.fna -* HISAT2_index: /import1/hisat2-index/mm10_CCDS/mm10_CCDS_nucleotide.20140407_BALBc -* Cluster file: /import1/CCDS/Mm38.1/CCDS_nucleotide.20140407.fna_transcriptID_geneName.txt - -**hg19** - -* GTF file: /import1/CCDS/HsGRCh37.1/HsGRCh37.1_CCDS_nucleotide.20131129.fa.GTF -* TMAP_index: /import1/tmap-index/tmap3.4.1/hg19/hg19_CCDS_nucleotide.20131129.fa -* HISAT2_index: /import1/hisat2-index/hg19/hg19_CCDS_nucleotide.20131129.fna -* Cluster file: /import1/CCDS/HsGRCh37.1/HsGRCh37.1_CCDS.20131129_transcriptID_geneName.txt - -**hg38** - -* GTF file: /import1/CCDS/GRCh38.p2/GRCh38.p2_CCDS_nucleotide.20150512.fna.GTF -* TMAP_index: /import1/tmap-index/tmap3.4.1/hg38/hg38_CCDS_nucleotide.20150512.fna -* HISAT2_index: /import1/hisat2-index/hg38_CCDS_downloadedRef/h19_CCDS_nucleotide.20150512.fna -* Cluster file: /import1/CCDS/GRCh38.p2/GRCh38.p2_CCDS.20150512_transcriptID_geneName.txt ------ - - </help> </tool> - - |
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| diff -r be08c88b353e -r cff0a5f324d4 isoem2_isode2/tool_data_table_conf.xml --- a/isoem2_isode2/tool_data_table_conf.xml Sun Mar 26 22:27:30 2017 -0400 +++ b/isoem2_isode2/tool_data_table_conf.xml Sat Apr 01 10:59:38 2017 -0400 |
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| @@ -1,10 +1,10 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changedin revision 4550:535d276c92bc--> -<tables> - <!-- Locations of genome/transcriptome indices, genome file, fastq file, GTF file, etc for Epi-Seq --> - <table name="IsoEM" comment_char="#"> - <columns>value, GTF, CCDS_INDEX, Cluster </columns> - <file path="tool-data/IsoEM.loc" /> - </table> - -</tables> - +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changedin revision 4550:535d276c92bc--> +<tables> + <!-- Locations of genome/transcriptome indices, genome file, fastq file, GTF file, etc for Epi-Seq --> + <table name="IsoEM" comment_char="#"> + <columns>value, GTF, TMAP_INDEX, HISAT2_INDEX, Cluster </columns> + <file path="tool-data/IsoEM.loc" /> + </table> + +</tables> + |
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| diff -r be08c88b353e -r cff0a5f324d4 isoem2_isode2/tool_data_table_conf.xml.sample --- a/isoem2_isode2/tool_data_table_conf.xml.sample Sun Mar 26 22:27:30 2017 -0400 +++ b/isoem2_isode2/tool_data_table_conf.xml.sample Sat Apr 01 10:59:38 2017 -0400 |
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| @@ -1,10 +1,10 @@ -<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changedin revision 4550:535d276c92bc--> -<tables> - <!-- Locations of genome/transcriptome indices, genome file, fastq file, GTF file, etc for Epi-Seq --> - <table name="IsoEM" comment_char="#"> - <columns>value, GTF, CCDS_INDEX, Cluster </columns> - <file path="tool-data/IsoEM.loc" /> - </table> - -</tables> - +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changedin revision 4550:535d276c92bc--> +<tables> + <!-- Locations of genome/transcriptome indices, genome file, fastq file, GTF file, etc for Epi-Seq --> + <table name="IsoEM" comment_char="#"> + <columns>value, GTF, TMAP_INDEX, HISAT2_INDEX, Cluster </columns> + <file path="tool-data/IsoEM.loc" /> + </table> + +</tables> + |