singularity for HiC Pro

[tanasa]

Dear Nicolas,

would you please also let me know, which is the latest singularity container that I shall use (and shall i pull down the docker container and convert it into a singularity image ?). As of now, I am encountering the following issue :

singularity exec hicpro_latest_ubuntu_04dec2020.img HiC-Pro -c config_test_latest.2.txt -i test_data -o test_data_results
INFO:    Converting SIF file to temporary sandbox...
WARNING: underlay of /etc/localtime required more than 50 (81) bind mounts
/home/btanasa/test_data_results folder alreads exists. Do you want to overwrite it ? (y/n) [n] : 
y

Run HiC-Pro 2.11.4
--------------------------------------------
Tue Aug 17 16:55:56 PDT 2021
Bowtie2 alignment step1 ...
Logs: logs/dixon_2M/mapping_step1.log
Exit: Error in reads alignment - Exit
make: *** [/usr/local/bin/HiC-Pro_2.11.4/bin/../scripts//Makefile:88: bowtie_global] Error 1
INFO:    Cleaning up image...

[tanasa]

Hi Nicolas, I have rebuild a singularity container by using the following docker image :

singularity build hicpro3.simg docker://nservant/hicpro:3.0.0

However, when I do exec the simg, I am getting the following message :

[btanasa@cfx22885s-srcf-d11-13-east ARIMA_HiC_now_analysis_HIC_PRO]$ singularity exec hicpro3.simg HiC-Pro
INFO:    Converting SIF file to temporary sandbox...
WARNING: underlay of /etc/localtime required more than 50 (78) bind mounts
FATAL:   "HiC-Pro": executable file not found in $PATH
INFO:    Cleaning up image..

Any suggestions please ?

[nservant]

Hi @tanasa Could you try to build the singularity from the Singularity file which is within the HiC-Pro repo ? Also, I'll release very soon the version 3.1.0, so maybe you can try this later version directly ? Best N

[tanasa]

Merci Nicolas. I can see that the version 3.1 is described on : https://github.com/nservant/HiC-Pro

if the docker container for the version 3.1 is available on docker.hub, please let me know and I could convert it into a singularity container for SLURM. Thank you very much.

[nservant]

Hi @tanasa I'm currently working on the Docker/Singlarity of the 3.1.0 version I'll let you know as soon as I have something ready ! Thanks

[nservant]

Hi @tanasa Just to let you know that I released a new HiC-Pro version with a new Singularity recipe. Best

[tanasa]

wonderful, thanks Nicolas.

[tanasa]

Hi Nicolas. Thank you for our previous conversations.

I have not found the Docker/Singularity 3.1.0 on Docker Hub : where shall I look for it ? Thank you !

~ Bogdan