BAM(1) User Commands BAM(1)NAME
bam - fast and flexible build system
SYNOPSIS
bam [OPTION]... [VARIABLE=VALUE]... [TARGET]...
DESCRIPTION
Builds applications using the bam build system.
Execution:
-a abort on error
-c clean targets
-d build targets that is dependent given targets
--dry dry run, don't run any jobs
-j sets the number of threads to use (default: 0, disabled)
-s bam file to use (default: bam.lua)
Lua:
-l print local variables in backtrace
-t print backtrace when an error occurs
Output:
-r build progress report format (default: s) b = progress bar c = use ansi colors s = build steps
-v be verbose
Other:
-n don't use cache
-h, --help
prints this help
Debug:
--debug-nodes
prints all the nodes with dependencies
--debug-detail
prints all the nodes with dependencies and details
--debug-jobs
prints all the jobs that exist
--debug-dot
prints all nodes as a graphviz dot file
--debug-jobs-dot
prints all jobs as a graphviz dot file
--debug-trace-vm
prints a line for every instruction the vm makes
--debug-dump-int
prints the internals scripts to stdout
--debug-no-int
don't load internal scripts
bam by Magnus Auvinen (magnus.auvinen@gmail.com)
bam May 2011 BAM(1)
Check Out this Related Man Page
orte-clean(1) Open MPI orte-clean(1)NAME
orte-clean - Cleans up any stale processes and files leftover from Open MPI jobs.
SYNOPSIS
orte-clean [--verbose]
mpirun --pernode [--host | --hostfile file] orte-clean [--verbose]
OPTIONS
[-v | --verbose] This argument will run the command in verbose mode and print out the universes that are getting cleaned up as well as pro-
cesses that are being killed.
DESCRIPTION
orte-clean attempts to clean up any processes and files left over from Open MPI jobs that were run in the past as well as any currently
running jobs. This includes OMPI infrastructure and helper commands, any processes that were spawned as part of the job, and any temporary
files. orte-clean will only act upon processes and files that belong to the user running the orte-clean command. If run as root, it will
kill off processes belonging to any users.
When run from the command line, orte-clean will attempt to clean up the local node it is run from. When launched via mpirun, it will clean
up the nodes selected by mpirun.
EXAMPLES
Example 1: Clean up local node only.
example% orte-clean
Example 2: To clean up on a specific set of nodes specified on command line, it is recommended to use the pernode option. This will run
one orte-clean for each node.
example% mpirun --pernode --host node1,node2,node3 orte-clean
To clean up on a specific set of nodes from a file.
example% mpirun --pernode --hostfile nodes_file orte-clean
Example 3: Within a resource managed environment like N1GE, SLURM, or Torque. The following example is from N1GE.
First, we see that we have two nodes with two CPUs each.
example% qsh -pe orte 4
example% mpirun -np 4 hostname
node1
node1
node2
node2
Clean up all the nodes in the cluster.
example% mpirun --pernode orte-clean
Clean up a subset of the nodes in the cluster.
example% mpirun --pernode --host node1 orte-clean
SEE ALSO orterun(1), orte-ps(1)1.4.5 Feb 10, 2012 orte-clean(1)
Hi,
I'm porting code from Windows to HP-UX 11, compiling with g++.
I'm getting a compilation error on the system's debug.h include file, which is included very indirectly through a series of other system include files. The one I am including is <map> .
The errors I am getting are:... (4 Replies)
All,
We need to run multiple jobs in parallel with the dependencies intact.
I was trying to use the same with &, but in vain. Is there is any other way to resolve this issue.
I need to run
Set1
A.sh
B.sh
C.sh
Set2
D.sh
E.sh
Set3
F.sh (10 Replies)
Hi,
I have this script, searches and sets variables, then searches and sets more variables from multiple files.
I'd need to debug it a bit.
#!/bin/bash
egrep $1 `find | grep MAGT` >/tmp/resRA-$$
thread=`sed -n '/{0x/ {s/^.*{0x\(*\).*/\1/p;q}' /tmp/resRA-$$`
tag=`sed -n '/Tag=/... (5 Replies)
Is there a way to see or print a sub code?
Sometime a sub could be already defined, but in the debug mode (so, interactively) it could be already out of screen.
So, I would think about a way to check if the sub is defined (just 'defined' is not a problem) and how it is defined.
Also, if... (4 Replies)
Trying to clean up the last little thing in this script which is that the mv always performs no matter whether it is needed or not. It doesn't cause any bugs just prints an unsightly "can't mv source and dest are the same". Obviously I want to get rid of it but having issues getting the... (4 Replies)
Hi,
I have a file in PERL in the following pattern
filename| 06-Dec-11 03.04.14.000000 PM
filename1| 06-Dec-11 05.05.14.000000 PM
I need to replace .(dot) with :(semicolon) in the timestamp value of the file
How can this be done. Any help will be appreciated
Thanks in advance (5 Replies)
Hey gyuz,
I wanna calculate the number of mapped reads of a bam file in a region of interest. I used this code to do so :
samtools view input.bam chrname:region1 > region1.txt
This will store all the reads from given bam file within the region of interest in region1.txt
Now I have... (5 Replies)
Hi,
I'm running a rdt (run dot tcl) command, and come accross this line:
alias abc 'set ARGS =(\!*); source home123/abc/$ARGS/setup'
What does the command exactly do?
Please help. (6 Replies)
hello,
i would need a fast awk script for conversion of network formats (from 'sif' to 'adjacency' format):
sif (pp means only: protein-protein interaction):
A pp B
A pp C
B pp D
D pp E
in an adjacency n x n matrix:
A B C D E
A 0 1 1 0 0
B 1 0 0 1 0
C 1 0 0 0 0
D 0 1 0 0 1... (10 Replies)
i have tried process substitution, but run in some problems.
this works:
samtools view -h $SAMdir/$b.bam | htseq-count -m union -s no -q -t exon -i gene_id - $gtf > $b.count &
but this not:
htseq-count -m union -s no -q -t exon -i gene_id <(samtools view -h $SAMdir/$b.bam) $gtf >... (7 Replies)
Hi, I have tab-deliminated data similar to the following:
dot is-big 2
dot is-round 3
dot is-gray 4
cat is-big 3
hot in-summer 5
I want to count the frequency of each individual "unique" value in the 1st column. Thus, the desired output would be as follows:
dot 3
cat 1
hot 1
is... (5 Replies)
I am trying to create a code that will use all the bam files stored on a separate drive (/media/cmccabe/C2F8EFBFF8EFAFB9/pool_I_090215), run them in a program that I have changed the directory to, and the output gets re-directed to (/home/cmccabe/Desktop/NGS/pool_I_090215). I have tried the... (11 Replies)
Is there a way to use a directory with multiple files (.bam) to create one new file? The below bash loop will create a new file (header.sam) for each of the bam files. However, I only need to use 1 of the bam file to make 1 header file. I attempted a code as well, but not sure if thats... (5 Replies)
Hi,
Can anyone help with the below please?
I have written some code which takes an input file, and and prints the contents out to a new file - it then loops round and prints the same columns, but increments the ID column by 1 each time.
Input file;
NAME,1,15-Dec-15,
NAME,1,21-Dec-15,... (9 Replies)