Entering edit mode
5.9 years ago
Bioinfonext
▴
470
Hi,
I am want to use ea-utils fastq-join to join multiple amplicon sequencing pair end read.
I am working on HPC server but I have installed myself ea-utils as it is not available on server.
so the path for ea-utils is:
/users/3052/Amplicon_data/ITS_analysis/ITS/ExpressionAnalysis-ea-utils-bd148d4/clipper/fastq-join
and multiple fast files names are like this:
Soil-7_S32_L001_R1_001.fastq.gz Soil-7_S32_L001_R2_001.fastq.gz
Soil-8_S32_L001_R1_001.fastq.gz Soil-8_S32_L001_R2_001.fastq.gz
Soil-9_S42_L001_R1_001.fastq.gz Soil-9_S42_L001_R2_001.fastq.gz
Now, How should I run bash scripts loop to join the multiple files in a single command?
Thanks in advance.
What have you tried? Or do you just need someone to do all the analysis for you?
I am trying to use below job scripts but I am not sure If any tool is not available on server then how to load tool in job script which is installed in my own directory, should I use module load or what I have to do exactly?
Thanks
Noone here knows your exact system, but generally using the full path to a software binary which is correctly installed if necessary and visible to all cluster nodes - i.e on a shared storage - should work.
Module load won't help if the software is not installed on your cluster.
Good luck!
If
fastq-join
is located as/users/3052/Amplicon_data/ITS_analysis/ITS/ExpressionAnalysis-ea-utils-bd148d4/clipper/fastq-join
, use that location in place of/mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join
in the last three lines.If it is located in
/mnt/scratch/users/staffnumber/ea-utils.1.1.2-537/fastq-join
, remove themodule load
line.The concept is well explained by colindaven.
module load
will only work for modulefiles located in$MODULEPATH
, not for custom binaries.