From: Diane Trout <diane@caltech.edu>
Date: Tue, 8 Sep 2015 23:36:25 +0000 (-0700)
Subject: add some documentation -- shocking I know
X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=commitdiff_plain;h=d9f9796cfbbf9caa76285a550adb28acf1898a58;p=htsworkflow.git

add some documentation -- shocking I know
---

diff --git a/README.txt b/README.txt
new file mode 100644
index 0000000..6571d17
--- /dev/null
+++ b/README.txt
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+Introduction
+============
+
+This contains our LIMS system and a collections of utilities
+to help manage curation and submission of data.
+
+Fastq Conversion
+----------------
+
+Over time there were several different attempts to capture
+and store "fastq-like" data. HTS-Workflow has at one time or
+another supported NCBI srf files, Illumina qseq files, and 
+fastq files.
+
+Because all of the current submitting agencies want fastq files.
+There are some utilities to convert whatever is stored in our sequence 
+archive to fastq files.
+
+The current ENCODE submission script is encode_submission/encode3.py
+and it has a --fastq option that given a mapping file will try to 
+go find all the flowcells and generate condor scripts using
+the lower level conversion utilities 
+
+ * htsworkflow/pipelines/desplit_fastq.py
+ * htsworkflow/pipelines/qseq2fastq.py
+ * htsworkflow/pipelines/srf2fastq.py
+
+desplit_fastq converts a list of fastq files into a single fastq file.
+qseq2fastq takes a collection of qseq files or a tar-file containing 
+qseq files and converts it into a fastq file. and srf2fastq converts
+the NCBI srf files. 
+
+Note: srf2fastq depends on the stadenio tools.
+
+The encode3.py --fastq mode reads a mapping file that contains
+
+library_id destination_directory
+
+encode3.py has a '--compression gzip'  option for if you want the
+resulting fastq file to be compressed as a gzip file.
+
+