Mercurial > repos > kevyin > fastq_groomer_parallel

changeset 5:4983170729cc

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
README
author Kevin Ying <k.ying@garvan.org.au>
date Fri, 14 Sep 2012 11:01:34 +1000
parents 28a0718eb9e7
children 5108dc779c01
files README fastq_groomer_parallel.py
diffstat 2 files changed, 21 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Sep 14 11:01:34 2012 +1000
@@ -0,0 +1,21 @@
+Copyright (c) 2012, Kenneth Sabir
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+        Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+        Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+        Neither the name of the Garvan Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+##################################################
+Installation:
+#================================================#
+
+Tested on -r e6444e7a1685
+This currently depends on the following galaxy_utils python library which should come with the default galaxy install
+
+More info:
+    from galaxy_utils.sequence.fastq import fastqReader, fastqVerboseErrorReader, fastqAggregator, fastqWriter
+##################################################
--- a/fastq_groomer_parallel.py	Thu Sep 13 04:33:58 2012 -0400
+++ b/fastq_groomer_parallel.py	Fri Sep 14 11:01:34 2012 +1000
@@ -1,17 +1,5 @@
 # Kenneth Sabir
 # Garvan Institute
-
-# Copyright (c) 2012, Kenneth Sabir
-# All rights reserved.
-# 
-# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-# 
-#         Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-#             Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-#                 Neither the name of the Garvan Institute nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
-# 
-#                 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
 import sys
 import time
 import os