Hi,
I'm Natalja from EMBL-EBI. We are trying to run NGSeasy pipeline on our Embassy Cloud and I found someissues. Would like to notice that I'm not a bash script expert, so may be I just misunderstood smth or there are differences in scripts execution on different linux distributions.
We are using CentOS as NFS server where NGSeasy scripts are stored and some of them are running (project initiation scripts) and Ubuntu 14.04 for docker machines.
Here is my list:
1) variable VERSION is missed error almost in all scripts. I've fixed it by renaming VERSION to NGSEASYVERSION (from config file)
2) function logger_ngseasy() in some of the scripts was causing an error because it is called from inside the script(s) with only one argument passed (at least as I understood). So I've changed it by adding default value for the second argument "mylogfile".
3) I've commented out in all scripts the following line:
since it was causing errors.
4) not sure that it is an issue, but in order to run scripts from NFS server I've changed the call of the scripts from /bin/bash Githubissues.
Githubissues is a development platform for aggregating issues.
Hi, I'm Natalja from EMBL-EBI. We are trying to run NGSeasy pipeline on our Embassy Cloud and I found someissues. Would like to notice that I'm not a bash script expert, so may be I just misunderstood smth or there are differences in scripts execution on different linux distributions. We are using CentOS as NFS server where NGSeasy scripts are stored and some of them are running (project initiation scripts) and Ubuntu 14.04 for docker machines.
Here is my list: 1) variable VERSION is missed error almost in all scripts. I've fixed it by renaming VERSION to NGSEASYVERSION (from config file) 2) function logger_ngseasy() in some of the scripts was causing an error because it is called from inside the script(s) with only one argument passed (at least as I understood). So I've changed it by adding default value for the second argument "mylogfile". 3) I've commented out in all scripts the following line:
logger_ngseasy "[${NGSEASY_STEP}]:CMD: awk 'NR >1 {print $5"/"$1}' ${config_tsv} | sort | uniq > ${HOME}/ngseasy_tmp/Project_list" ${config_run_log}
since it was causing errors. 4) not sure that it is an issue, but in order to run scripts from NFS server I've changed the call of the scripts from /bin/bash Githubissues.