uiuc_igb_scripts.git
2 years agoadd readme for uiuc_igb_scripts master
Don Armstrong [Thu, 13 Jul 2017 21:16:38 +0000 (14:16 -0700)]
add readme for uiuc_igb_scripts

2 years agothe shell must be specified last
Don Armstrong [Tue, 27 Jun 2017 17:23:41 +0000 (10:23 -0700)]
the shell must be specified last

2 years agoslurm interactive jobs need --pty, a shell, and srun
Don Armstrong [Tue, 27 Jun 2017 17:22:26 +0000 (10:22 -0700)]
slurm interactive jobs need --pty, a shell, and srun

2 years agosilence "which sbatch" checking
Don Armstrong [Mon, 26 Jun 2017 15:18:56 +0000 (08:18 -0700)]
silence "which sbatch" checking

2 years agofix sbatch array options
Don Armstrong [Tue, 6 Jun 2017 20:10:04 +0000 (13:10 -0700)]
fix sbatch array options

2 years agooutput correct job submitter in interactive debug
Don Armstrong [Tue, 6 Jun 2017 20:09:51 +0000 (13:09 -0700)]
output correct job submitter in interactive debug

2 years agosupport precommands before running scripts
Don Armstrong [Tue, 6 Jun 2017 19:03:58 +0000 (12:03 -0700)]
support precommands before running scripts

2 years agoslurm writes output to the same file by default
Don Armstrong [Wed, 8 Feb 2017 19:03:10 +0000 (11:03 -0800)]
slurm writes output to the same file by default

2 years agoslurm options are braindead and require =
Don Armstrong [Wed, 8 Feb 2017 19:02:15 +0000 (11:02 -0800)]
slurm options are braindead and require =

2 years agono need to use = for long options
Don Armstrong [Wed, 8 Feb 2017 19:01:13 +0000 (11:01 -0800)]
no need to use = for long options

2 years agofix $? test for batch option
Don Armstrong [Wed, 8 Feb 2017 18:58:20 +0000 (10:58 -0800)]
fix $? test for batch option

2 years agofix slurm typo
Don Armstrong [Wed, 8 Feb 2017 18:57:53 +0000 (10:57 -0800)]
fix slurm typo

2 years agosbatch reads from STDIN by default
Don Armstrong [Wed, 8 Feb 2017 18:55:47 +0000 (10:55 -0800)]
sbatch reads from STDIN by default

2 years agosupport slurm
Don Armstrong [Wed, 8 Feb 2017 18:52:13 +0000 (10:52 -0800)]
support slurm

3 years agoonly escape if the command contains a space
Don Armstrong [Fri, 8 Jul 2016 20:09:15 +0000 (13:09 -0700)]
only escape if the command contains a space

3 years agotweak -N sanitation
Don Armstrong [Fri, 8 Jul 2016 20:01:58 +0000 (13:01 -0700)]
tweak -N sanitation

3 years agosanitize -N
Don Armstrong [Fri, 8 Jul 2016 20:00:27 +0000 (13:00 -0700)]
sanitize -N

3 years agoadd --join option
Don Armstrong [Mon, 27 Jun 2016 21:36:21 +0000 (14:36 -0700)]
add --join option

3 years agosupport account option -A
Don Armstrong [Mon, 27 Jun 2016 19:15:37 +0000 (12:15 -0700)]
support account option -A

4 years agoadd support for more -l options to qsub
Don Armstrong [Thu, 6 Aug 2015 21:11:13 +0000 (14:11 -0700)]
add support for more -l options to qsub

4 years agoautomatically specify a job name (no more STDIN)
Don Armstrong [Wed, 5 Aug 2015 20:15:35 +0000 (13:15 -0700)]
automatically specify a job name (no more STDIN)

4 years agoallow for running all array items in one job
Don Armstrong [Wed, 5 Aug 2015 20:00:02 +0000 (13:00 -0700)]
allow for running all array items in one job

4 years agohandle running multiple array options in each job to work around low queue limits
Don Armstrong [Wed, 5 Aug 2015 19:47:54 +0000 (12:47 -0700)]
handle running multiple array options in each job to work around low queue limits

4 years agofixup array slot limit
Don Armstrong [Wed, 5 Aug 2015 17:16:53 +0000 (10:16 -0700)]
fixup array slot limit

4 years agoadd array slot limit
Don Armstrong [Wed, 5 Aug 2015 17:15:52 +0000 (10:15 -0700)]
add array slot limit

4 years agoadd missing _ in here doc end
Don Armstrong [Wed, 5 Aug 2015 17:05:01 +0000 (10:05 -0700)]
add missing _ in here doc end

4 years agoremove die because we now support array options
Don Armstrong [Wed, 5 Aug 2015 17:04:13 +0000 (10:04 -0700)]
remove die because we now support array options

4 years agoadd support for array options
Don Armstrong [Wed, 5 Aug 2015 17:02:04 +0000 (10:02 -0700)]
add support for array options

4 years agomem needs to be concatenated, not separated with ,
Don Armstrong [Wed, 5 Aug 2015 16:44:53 +0000 (09:44 -0700)]
mem needs to be concatenated, not separated with ,

4 years agospecify the -I option correctly
Don Armstrong [Wed, 5 Aug 2015 16:44:20 +0000 (09:44 -0700)]
specify the -I option correctly

4 years agoactually return the qsub options
Don Armstrong [Wed, 5 Aug 2015 16:43:16 +0000 (09:43 -0700)]
actually return the qsub options

4 years agoavoid using Pod::Simple because biocluster doesn't have it installed in the system...
Don Armstrong [Wed, 5 Aug 2015 16:43:08 +0000 (09:43 -0700)]
avoid using Pod::Simple because biocluster doesn't have it installed in the system perl

4 years agomake dqsub executable
Don Armstrong [Wed, 5 Aug 2015 16:38:00 +0000 (11:38 -0500)]
make dqsub executable

4 years agofix two typos in dqsub
Don Armstrong [Wed, 5 Aug 2015 16:37:01 +0000 (09:37 -0700)]
fix two typos in dqsub

4 years agoadd start of dqsub
Don Armstrong [Wed, 5 Aug 2015 16:36:27 +0000 (09:36 -0700)]
add start of dqsub

4 years agotweak the invocation slightly
Don Armstrong [Mon, 27 Jul 2015 14:55:43 +0000 (09:55 -0500)]
tweak the invocation slightly

4 years agoadd the option to give a -j to make
Don Armstrong [Mon, 27 Jul 2015 14:53:29 +0000 (09:53 -0500)]
add the option to give a -j to make

4 years agofix if statement
Don Armstrong [Wed, 27 May 2015 20:16:09 +0000 (13:16 -0700)]
fix if statement

4 years agoadd make
Don Armstrong [Wed, 27 May 2015 20:13:06 +0000 (13:13 -0700)]
add make

4 years agoonly e-mail on abort
Don Armstrong [Tue, 26 May 2015 21:26:13 +0000 (14:26 -0700)]
only e-mail on abort

4 years agowe can only request 18GB
Don Armstrong [Tue, 26 May 2015 19:03:04 +0000 (12:03 -0700)]
we can only request 18GB

4 years agoadd destination directory
Don Armstrong [Tue, 26 May 2015 18:25:59 +0000 (11:25 -0700)]
add destination directory

4 years agostop immediately upon error
Don Armstrong [Tue, 26 May 2015 18:24:25 +0000 (11:24 -0700)]
stop immediately upon error

4 years agoreserve 32GB of ram
Don Armstrong [Tue, 26 May 2015 18:11:32 +0000 (11:11 -0700)]
reserve 32GB of ram

4 years agosend mail when the job ends
Don Armstrong [Tue, 26 May 2015 17:30:22 +0000 (10:30 -0700)]
send mail when the job ends

4 years agouse - for stdin
Don Armstrong [Tue, 26 May 2015 17:29:13 +0000 (10:29 -0700)]
use - for stdin

4 years agowe want samtools 1.0, not samtools 0.1.8
Don Armstrong [Tue, 26 May 2015 17:09:21 +0000 (10:09 -0700)]
we want samtools 1.0, not samtools 0.1.8

4 years agocompress fastq
Don Armstrong [Tue, 26 May 2015 16:48:01 +0000 (09:48 -0700)]
compress fastq

4 years agoload samtools
Don Armstrong [Tue, 26 May 2015 16:46:53 +0000 (09:46 -0700)]
load samtools

4 years agouse rsync instead of wget
Don Armstrong [Tue, 26 May 2015 16:25:08 +0000 (09:25 -0700)]
use rsync instead of wget

4 years agofix wrong SRR variable name
Don Armstrong [Tue, 26 May 2015 16:21:57 +0000 (09:21 -0700)]
fix wrong SRR variable name

4 years agoquote variables
Don Armstrong [Tue, 26 May 2015 16:21:25 +0000 (09:21 -0700)]
quote variables

4 years agoadd missing space
Don Armstrong [Tue, 26 May 2015 16:20:23 +0000 (09:20 -0700)]
add missing space

4 years agofix variable names which were wrong
Don Armstrong [Tue, 26 May 2015 16:19:36 +0000 (09:19 -0700)]
fix variable names which were wrong

4 years agoadd fpkm script
Don Armstrong [Tue, 26 May 2015 16:16:16 +0000 (09:16 -0700)]
add fpkm script