ERROR ---> SAMTOOLS path not given correctly in AllimOptions file
Allelic imbalance meter (Allim), a new tool for measuring allele speci
Brought to you by:
ramvinay
Menu
▾
▴
#1 ERROR ---> SAMTOOLS path not given correctly in AllimOptions file
New
nobody
None
Medium
Defect
2013-07-13
2013-07-09
Anonymous
No
Originally created by: richard....@gmail.com
I'm trying to validate my installation using the test data set
when I enter:
python ./Allim.py --option-file AllimOptions_2Pexpr
I get:
ERROR ---> SAMTOOLS path not given correctly in AllimOptions file
I'm using the default AllimOptions_2Pexpr file with the line
SAMTOOLS = /Allim_1.0/executables/samtools
I've also tried changing to:
/samtools-0.1.18/samtools
I'm using Mac Os X 10.6.8
python 2.7.3
samtools-0.1.18
View and moderate all "tickets Discussion" comments posted by this user
Mark all as spam, and block user from posting to "Tickets"
Originally posted by: ramvinayp@gmail.com
could you please drage samtools on terminal and see if it runs out side Allim?
View and moderate all "tickets Discussion" comments posted by this user
Mark all as spam, and block user from posting to "Tickets"
Originally posted by: richard....@gmail.com
I just tried
cd samtools-0.1.18/examples
samtools faidx ex1.fa
samtools import ex1.fa.fai ex1.sam.gz ex1.bam
[sam_header_read2] 2 sequences loaded.
samtools index ex1.bam
samtools tview ex1.bam ex1.fa
and i get an alignment, so it looks like it runs fine outside of Allim