Problems installing LoReAn
csijcs opened this issue · 8 comments
I am trying to install LoReAn on Ubuntu using singularity 2.6.0 accoring to the following bash script:
singularity pull --name mysql.simg shub://ISU-HPC/mysql
wget -O ~/.my.cnf https://raw.githubusercontent.com/lfaino/LoReAn/master/third_party/conf_files/my.cnf
wget -O ~/.mysqlrootpw https://raw.githubusercontent.com/lfaino/LoReAn/master/third_party/conf_files/mysqlrootpw
mkdir -p ${HOME}/mysql/var/lib/mysql ${HOME}/mysql/run/mysqld
singularity instance.start --bind ${HOME} --bind ${HOME}/mysql/var/lib/mysql/:/var/lib/mysql --bind ${HOME}/mysql/run/mysqld:/run/mysqld ./mysql.simg mysql
singularity run instance://mysql
singularity shell --bind ${HOME}/mysql/run/mysqld:/run/mysqld/ docker://lfaino/lorean
cat ~/.bashrc /opt/LoReAn/third_party/conf_files/pathToExport.txt > ~/.bashrc.lorean
source ~/.bashrc.lorean
cp -r /opt/LoReAn/third_party/software/augustus/ ~/
I keep getting the following error:
ERROR : Failed to resolve path to /home/csijcs/anaconda2/var/singularity/mnt/container: No such file or directory ABORT : Retval = 255 ERROR : Daemon failed to start ABORT : Retval = -1 ERROR: A daemon process is not running with this name: mysql ABORT: Aborting with RETVAL=255
Can you please tell me what I'm going wrong?
Hi,
From what i can see, mysql is not running. Additionally, the path that you reported is a bit strange.
at which step of the installation you get this error?
Basically right in the beginning. I can't sudo adduser lorean because its a shared server, and I've put the gm_key in my home directory. Then I run the script above and get the error
to me this path is a bit strange.
"/home/csijcs/anaconda2/var/singularity/mnt/container"
does it exists?
I agree the path is strange and don't know how to change it in the program. Singluarity is actually installed in /home/csijcs/anaconda2/bin. /home/csijcs/anaconda2/var does exist, but noting related to singularity is installed there
I always use the instruction ia this site to install singularity option 1:
https://singularity.lbl.gov/install-linux
I've tried installing through that route and run into problems because I'm not a sudo user. I installed through conda and singularity seems to run find. Is this an issue with singularity or with LoReAn?
i will try to install via conda and see.
i let you know