diff flaimapper.xml @ 19:ab3ea877607f draft

Uploaded

--- a/flaimapper.xml	Fri Mar 20 10:45:21 2015 -0400
+++ b/flaimapper.xml	Fri Mar 20 11:14:32 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.4.a">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
-		<requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
-		<requirement type="package" version="1.1.4">flaimapper</requirement>
+		<requirement type="package" version="0.8.2.1">pysam</requirement>
+		<requirement type="package" version="1.1.5">flaimapper</requirement>
 	</requirements>
 	
 	<version_command>flaimapper --version</version_command>
@@ -62,6 +62,21 @@
 
 The reference sequence should be provided in FASTSA format.
 
+You can access **ncRNAdb09** at the following URLs:
+https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
+https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
+
+Therefore you need bam files aligned to the same reference. We have made
+the following available:
+
+ - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
+ - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
+
+If you want to test flaimapper with example data you can obtain several
+alignment files from this following directory tree:
+
+https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
+
 Installation
 ------------
 
@@ -77,7 +92,7 @@
 
 **pysam**:
 
-The MIT License (>=3)
+The MIT License
 
 Contact
 -------