roryk

STAR version=STAR_2.4.0e
STAR compilation time,server,dir=Fri Oct 24 10:43:53 EDT 2014 verona.cshl.edu:/sonas-hs/gingeras/nlsas_norepl/user/dobin/STAR/STAR.sandbox/source
##### DEFAULT parameters:
versionSTAR                       20201
versionGenome                     20101   20200   
parametersFiles                   -   
runMode                           alignReads
runThreadN                        1
genomeDir                         ./GenomeDir/
genomeLoad                        NoSharedMemory

roryk

Keybase proof

I hereby claim:

• I am roryk on github.
• I am roryk (https://keybase.io/roryk) on keybase.
• I have a public key whose fingerprint is 7C28 113B F748 6132 2854 81AD 06E8 EF6A D433 A483

To claim this, I am signing this object:

roryk

import gffutils
import os

gtf = "path/to/your/gtf/file"

def get_gtf_db(gtf, in_memory=False):
    db_file = ":memory:" if in_memory else gtf + ".db"
    if in_memory or not os.path.exists(db_file):
        db = gffutils.create_db(gtf, dbfn=db_file)
    if in_memory:

roryk

diff -rupN libmaus-0.0.104-release-20140221093548/src/libmaus/aio/PosixFdInput.hpp new/src/libmaus/aio/PosixFdInput.hpp
--- libmaus-0.0.104-release-20140221093548/src/libmaus/aio/PosixFdInput.hpp	2014-02-21 04:36:04.000000000 -0500
+++ new/src/libmaus/aio/PosixFdInput.hpp	2014-04-14 12:21:04.000000000 -0400
@@ -46,7 +46,10 @@ namespace libmaus
 			public:
 			static int getDefaultFlags()
 			{
+				#ifndef __APPLE__
 				return O_RDONLY|O_NOATIME|O_LARGEFILE;
+				#endif

roryk

diff -rupN libmaus-0.0.104-release-20140221093548/src/libmaus/aio/PosixFdInput.hpp new/src/libmaus/aio/PosixFdInput.hpp
--- libmaus-0.0.104-release-20140221093548/src/libmaus/aio/PosixFdInput.hpp     2014-02-21 04:36:04.000000000 -0500
+++ new/src/libmaus/aio/PosixFdInput.hpp        2014-04-14 12:21:04.000000000 -0400
@@ -46,7 +46,10 @@ namespace libmaus
                        public:
                        static int getDefaultFlags()
                        {
+                               #ifndef __APPLE__
                                return O_RDONLY|O_NOATIME|O_LARGEFILE;
+                               #endif

roryk

# to add latex equations to a Rmd file, enclose the equations using the $ $ syntax
# and run knit_equation on the Rmd file instead of knit
knit_equation = function(rmd, md) {
  require('knitr')
  require('RCurl')
  gist_url = 'https://gist.github.com/roryk/4476421/raw/d08080c206b5663e0451a5ef6c56635a0c6f0f17/gistfile1'
  #gist_url = 'https://gist.github.com/raw/4476421/d08080c206b5663e0451a5ef6c56635a0c6f0f17/gistfile1'
  tmp = tempfile()
  knit(rmd, tmp)
  f = file(md, "w")

roryk

<style TYPE="text/css">
code.has-jax {font: inherit; font-size: 100%; background: inherit; border: inherit;}
</style>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
    tex2jax: {
        inlineMath: [['$','$'], ['\\(','\\)']],
        skipTags: ['script', 'noscript', 'style', 'textarea', 'pre'] // removed 'code' entry
    }
});

roryk

; from http://newsgroups.derkeiler.com/Archive/Comp/comp.emacs/2005-12/msg00064.html saved for posterity
(defalias 'puffer-lesen 'eval-buffer-or-region-step-by-step)

(defun eval-buffer-or-region-step-by-step ()
"Stepps through region if activated, otherwise takes the whole buffer
evaluating last-sexp and messaging point. As `eval-last-sexp' exits
encountering an error, you may easily pick the last point.
Attention: Commands changing the current-buffer as `find-file' will
derail the check."
(interactive)