# HG changeset patch
# User saharlcc
# Date 1491058778 14400
# Node ID cff0a5f324d4faa449279ad0072dc5e57229fb8f
# Parent  be08c88b353e946422bd30840056d33e7796acfd
Uploaded

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
@@ -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
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
@@ -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>
 
 
-
-
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
@@ -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>
+
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
@@ -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>
+