dtrudg

emptyarr = []

Channel
  .from(emptyarr)
  .set { testchan }


process testproc {

  input:

dtrudg

-bash-4.1$ jstack -l 13606
Picked up _JAVA_OPTIONS: -Dhttp.proxyHost=proxy.swmed.edu -Dhttp.proxyPort=3128
2016-06-29 22:19:09
Full thread dump Java HotSpot(TM) 64-Bit Server VM (24.51-b03 mixed mode):

"Attach Listener" daemon prio=10 tid=0x00007fa478001000 nid=0x35cc waiting on condition [0x0000000000000000]
   java.lang.Thread.State: RUNNABLE

   Locked ownable synchronizers:
	- None

dtrudg

-bash-4.1$ cat .nextflow.log
Jun-29 22:15:56.636 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
Jun-29 22:15:56.688 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
Jun-29 22:15:56.688 [main] DEBUG nextflow.cli.Launcher - $> /cm/shared/apps/nextflow/0.20.1/bin/nextflow test.nextflow
Jun-29 22:15:56.688 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.20.1
Jun-29 22:15:56.689 [main] INFO  nextflow.cli.CmdRun - Launching test.nextflow
Jun-29 22:15:57.155 [main] DEBUG nextflow.Session - Session uuid: c95fb10b-1a83-4278-a005-753ebb1cd5a7
Jun-29 22:15:57.156 [main] DEBUG nextflow.Session - Executor pool size: 8
Jun-29 22:15:57.180 [main] DEBUG nextflow.cli.CmdRun - 
  Version: 0.20.1 build 3853

dtrudg

// Path to an input file, or a pattern for multiple inputs
// Note - $baseDir is the location of this workflow file main.nf
params.story = "$baseDir/../test_data/mobydick.txt"

stories = Channel.fromPath( params.story )

process uppercase {

    cpus 1

dtrudg

Sep-30 09:01:42.253 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
Sep-30 09:01:42.354 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
Sep-30 09:01:42.354 [main] DEBUG nextflow.cli.Launcher - $> ./nextflow -trace nextflow.executor run main.nf
Sep-30 09:01:42.416 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.22.2-SNAPSHOT
Sep-30 09:01:42.428 [main] INFO  nextflow.cli.CmdRun - Launching `main.nf` [reverent_easley] - revision: 8300612e43
Sep-30 09:01:42.437 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: nextflow.config
Sep-30 09:01:42.439 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /home2/dtrudgian/Git/astrocyte_example_wordcount/workflow/nextflow.config
Sep-30 09:01:42.763 [main] DEBUG nextflow.config.ConfigBuilder - Setting config profile: 'standard'
Sep-30 09:01:42.828 [main] DEBUG nextflow.Session - Session uuid: 38109f9f-02e8-4363-be75-d76cb141dccb
Sep-30 09:01:42.828 [main] DEBUG n

dtrudg

May-23 13:38:56.471 [main] DEBUG nextflow.cli.Launcher - Setting http proxy: [proxy.swmed.edu, 3128]
May-23 13:38:56.555 [main] DEBUG nextflow.cli.Launcher - Setting https proxy: [proxy.swmed.edu, 3128]
May-23 13:38:56.555 [main] DEBUG nextflow.cli.Launcher - $> /cm/shared/apps/nextflow/0.24.1-SNAPSHOT/bin/nextflow run rnaseq-cluster-slurm/main.nf --config /project/SCCC/DOrso_lab/s418665/config.txt --fasta genome.fa --gtf genes.gtf --lib p --readLen 75 --egs 2451960000 --strandInfo frFirstStrand --outdir results_star --aligner star
May-23 13:38:56.620 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 0.24.1-SNAPSHOT
May-23 13:38:56.655 [main] INFO  nextflow.cli.CmdRun - Launching `rnaseq-cluster-slurm/main.nf` [clever_roentgen] - revision: 95d562219a
May-23 13:38:56.668 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /project/SCCC/DOrso_lab/s418665/rnaseq-cluster-slurm/nextflow.config
May-23 13:38:56.670 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /project/SC

dtrudg

{
   "schemaVersion": 1,
   "name": "mulled/m4",
   "tag": "latest",
   "architecture": "",
   "fsLayers": [
      {
         "blobSum": "sha256:76a19142909d9dfb909830f351fbab911427efb219bf965994f828f84aba3e6d"
      },
      {

dtrudg

# Put the singularity image into a .tar.gz
singularity export ubuntu-blender.img > ubuntu-blender.tar
gzip ubuntu-blender.tar

# Get the SHA256 hash, which we'll use as a container name for Clair
sha256sum ubuntu-blender.tar.gz

# NOW - you need to upload the .tar.gz somewhere accessible over http from
# the Clair backend - it will pull it from there. I've used our BioHPC owncloud
# instance, so the image is available via an https URI.

dtrudg

diff -rupN gpm-1.20.7-orig/src/daemon/do_selection.c gpm-1.20.7-xclip/src/daemon/do_selection.c
--- gpm-1.20.7-orig/src/daemon/do_selection.c   2012-10-27 10:21:38.000000000 +1300
+++ gpm-1.20.7-xclip/src/daemon/do_selection.c  2014-07-29 13:40:19.546689653 +1200
@@ -19,18 +19,49 @@
  *
  ********/

+#include <sys/stat.h>
+#include <sys/wait.h>
 #include "headers/message.h"        /* messaging in gpm */

dtrudg

#!/bin/sh
# Support for a shared clipboard
(/usr/bin/Xvfb :0 >/dev/null 2>&1) &
sleep 1
DISPLAY=:0 /bin/VBoxClient --clipboard
/usr/local/sbin/gpm -m /dev/input/mice -t exps2