Details
-
Type:
Improvement
-
Status: Open (View Workflow)
-
Priority:
Minor
-
Resolution: Unresolved
-
Labels:None
-
Story Points:0.5
-
Epic Link:
Description
Both biolinux 7 (ubuntu 12.04) and Ross's Lubuntu (Ubuntu 13.04) return the following errors when attempting to run the igb.zip scripts.
$ sh run_igb.sh
run_igb.sh: 43: run_igb.sh: 0: not found
run_igb.sh: 54: run_igb.sh: VMARGS[0]=-Xmx1024m: not found
run_igb.sh: 56: run_igb.sh: VMARGS[0]=-Xms32m: not found
run_igb.sh: 59: run_igb.sh: [[: not found
run_igb.sh: 69: run_igb.sh: Bad substitution
In order to fix this, the user must use
$ bash run_igb.sh
or better yet
$ run_igb.sh
I think it would be a good idea to put a helper error at the top of the script in case someone (like me) runs run_igb.sh the incorrect way
Example: Just after !#
if [ ! "$BASH_VERSION" ] ; then
echo "Please do not use sh to run this script ($0), just execute it directly" 1>&2
exit 1
fi
#script idea found here
#http://stackoverflow.com/questions/17752204/is-there-a-way-to-force-a-shell-script-to-run-under-bash-instead-of-sh
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Summary | igb.zip linux scripts do not work | igb.zip linux run_igb.sh script does not work when called with sh |
| Assignee | Kyle Suttlemyre [ kyle ] | Ann Loraine [ aloraine ] |
| Priority | Major [ 3 ] | Minor [ 4 ] |
| Description |
sh run_igb.sh [ 4:50PM] run_igb.sh: 43: run_igb.sh: 0: not found run_igb.sh: 54: run_igb.sh: VMARGS[0]=-Xmx1024m: not found run_igb.sh: 56: run_igb.sh: VMARGS[0]=-Xms32m: not found run_igb.sh: 59: run_igb.sh: [[: not found run_igb.sh: 69: run_igb.sh: Bad substitution |
Both biolinux 7 (ubuntu 12.04) and Ross's Lubuntu (Ubuntu 13.04) return the following errors when attempting to run the igb.zip scripts. $ sh run_igb.sh run_igb.sh: 43: run_igb.sh: 0: not found run_igb.sh: 54: run_igb.sh: VMARGS[0]=-Xmx1024m: not found run_igb.sh: 56: run_igb.sh: VMARGS[0]=-Xms32m: not found run_igb.sh: 59: run_igb.sh: [[: not found run_igb.sh: 69: run_igb.sh: Bad substitution In order to fix this, the user must use $ bash run_igb.sh or better yet $ run_igb.sh I think it would be a good idea to put a helper error at the top of the script in case someone (like me) runs run_igb.sh the incorrect way Example: Just after !# if [ ! "$BASH_VERSION" ] ; then echo "Please do not use sh to run this script ($0), just execute it directly" 1>&2 exit 1 fi |
| Description |
Both biolinux 7 (ubuntu 12.04) and Ross's Lubuntu (Ubuntu 13.04) return the following errors when attempting to run the igb.zip scripts. $ sh run_igb.sh run_igb.sh: 43: run_igb.sh: 0: not found run_igb.sh: 54: run_igb.sh: VMARGS[0]=-Xmx1024m: not found run_igb.sh: 56: run_igb.sh: VMARGS[0]=-Xms32m: not found run_igb.sh: 59: run_igb.sh: [[: not found run_igb.sh: 69: run_igb.sh: Bad substitution In order to fix this, the user must use $ bash run_igb.sh or better yet $ run_igb.sh I think it would be a good idea to put a helper error at the top of the script in case someone (like me) runs run_igb.sh the incorrect way Example: Just after !# if [ ! "$BASH_VERSION" ] ; then echo "Please do not use sh to run this script ($0), just execute it directly" 1>&2 exit 1 fi |
Both biolinux 7 (ubuntu 12.04) and Ross's Lubuntu (Ubuntu 13.04) return the following errors when attempting to run the igb.zip scripts. $ sh run_igb.sh run_igb.sh: 43: run_igb.sh: 0: not found run_igb.sh: 54: run_igb.sh: VMARGS[0]=-Xmx1024m: not found run_igb.sh: 56: run_igb.sh: VMARGS[0]=-Xms32m: not found run_igb.sh: 59: run_igb.sh: [[: not found run_igb.sh: 69: run_igb.sh: Bad substitution In order to fix this, the user must use $ bash run_igb.sh or better yet $ run_igb.sh I think it would be a good idea to put a helper error at the top of the script in case someone (like me) runs run_igb.sh the incorrect way Example: Just after !# if [ ! "$BASH_VERSION" ] ; then echo "Please do not use sh to run this script ($0), just execute it directly" 1>&2 exit 1 fi #script idea found here #http://stackoverflow.com/questions/17752204/is-there-a-way-to-force-a-shell-script-to-run-under-bash-instead-of-sh |
| Issue Type | Bug [ 1 ] | Improvement [ 4 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | David Norris [ dcnorris ] |
| Story Points | 0.5 |
| Workflow | classic default workflow [ 14392 ] | Loraine Lab Workflow [ 14614 ] |
| Rank | Ranked higher |
| Epic Link | IGBF-439 [ 15497 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Rank | Ranked higher |