mr-c

git clone https://github.com/mr-c/khmer.git
cd khmer
git remote add ged https://github.com/ged-lab/khmer.git
cd ..
conda install pip
hash -r
pip install virtualenv
python2.7 -m virtualenv env
source env/bin/activate
cd khmer

mr-c

#!/usr/bin/env python

import sys
import screed

if len(sys.argv) != 4:
    print >>sys.stderr, "USAGE: compare.py <mutations.txt> <orig.fasta> <corrected.fasta>"
    sys.exit(1)

fp_out = open('fp.out', 'w')

mr-c

for threads in {1..12}
do echo Threads: ${threads}
sudo su -c "echo 3 > /proc/sys/vm/drop_caches"
/usr/bin/time load-into-counting.py --threads ${threads} --report-total-kmers null data/25k-casava1_8.fq.bz2
done  |& tee load-log2-readparser

mr-c

KSIZE= 30
HASH_SIZE= 4e8
N_HASHES= 4

all: estimated_probabilities.k$(KSIZE).txt

%.fastq.gz:
        wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172903/SRR172903.fastq.gz
        wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR172/SRR172902/SRR172902.fastq.gz

mr-c

Portable workflow and tool descriptions with the CWL

Moved to the Auditorium, Room 1005

Come to the Genome and Biomedical Sciences Facility @ UC Davis, Room 1005 at 09:00 on Friday, June 26th, 2015 to hear Michael R. Crusoe give a practice talk for his presentation for the Galaxy Community Conference and the Bioinformatics Open Source Conference.

Michael is the software engineer for C. Titus Brown's lab for Data Intensive Biology which recently relocated to U. C. Davis from Michigan State University. https://impactstory.org/MichaelRCrusoe

mr-c

running build_ext
test_simple_parser (sphinxcontrib.autoprogram.ScannerTestCase) ... ERROR
test_subcommands (sphinxcontrib.autoprogram.ScannerTestCase) ... ERROR
test_import_object (sphinxcontrib.autoprogram.UtilTestCase) ... ok

======================================================================
ERROR: test_simple_parser (sphinxcontrib.autoprogram.ScannerTestCase)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/sphinxcontrib/autoprogram.py", line 151, in test_simple_parser

mr-c

# Rackspace Ubuntu 14.04
# 500 MB too slow
# Trying 1 GB General Purpose v1

ssh -L 8080:localhost:8080 root@${host}
su ubuntu

cd
sudo apt-get update
sudo apt-get dist-upgrade

mr-c

rgiuly@ubuntu:~/cwl-workflows/workflows/lobSTR$ sudo
./lobSTR-workflow.cwl lobSTR-demo.json
/usr/local/bin/cwl-runner 1.0.20150929170517
Unhandled exception
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 202, in try_make_job
    for j in jobs:
  File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py",
line 126, in job

mr-c

Michael,

Your project may be a good candidate for Conservancy.  The only item
that gives me some pause is that we're typically a home for software
projects, not for standards, although I do see you have a reference
implementation.  Nevertheless, I think it's worth applying to
Conservancy.  Our application process is relatively informal.  The
materials are below:

######################################################################

mr-c

<?xml version="1.0" encoding="UTF-8"?>
<rdf:RDF
   xmlns:CommandLineBinding="https://w3id.org/cwl/cwl#CommandLineBinding/"
   xmlns:cwl="https://w3id.org/cwl/cwl#"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:sld="https://w3id.org/cwl/salad#"
>
  <rdf:Description rdf:nodeID="N4ef640f378484c3e91d651024cbb7202">
    <rdf:first>mem</rdf:first>
    <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>