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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Singularity image #478

Closed clagiamba closed 3 years ago

clagiamba commented 3 years ago

Hi, Indeed, the qusb script is not set up to run with Singularity. Running singularity exec should do the job. Does it work ? N

Originally posted by @nservant in https://github.com/nservant/HiC-Pro/issues/432#issuecomment-822212102

clagiamba commented 3 years ago

Hi, any luck with the Singularity image working? It seems to find the command, but it does not execute. Also tried inside "singularity shell hicpro_latest_ubuntu.img", Singularity> HiC-Pro -i INOUT -c CONFIG", but it does not seem to recognize the commands... I am wondering if to try to install the Singularity image in another way (? maybe through docker) or to try a different route all together... Thank you!

nservant commented 3 years ago

Hi @clagiamba Which Singularity image are you using please ? I just release a couple of days ago a new Singularity recipe (3.1.0). Could you try this one please ? N

clagiamba commented 3 years ago

Hi! thank you, I just tried the one linked in the main README (https://zerkalo.curie.fr/partage/HiC-Pro/singularity_images/hicpro_latest_ubuntu.img) but I have not tried creating the image myself - let me try doing that then...

nservant commented 3 years ago

Otherwise, on the same link (folder), you have the image of the 3.1.0 version, which is the latest one !

clagiamba commented 3 years ago

Thank you! This works great and it is very easy to use. Basically just by downloading the image and using in the script HiCPro_step1_hic.sh: "singularity exec hicpro_3.1.0_ubuntu.img HiC-Pro -i 3_hicpro/rawdata -o hic_results -c config_test_latest.txt". Thank you!