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oschwengers / asap

A scalable bacterial genome assembly, annotation and analysis pipeline
https://doi.org/10.1371/journal.pcbi.1007134
GNU General Public License v3.0
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asap/asap-docker.sh script can not be found in its container #8

Closed meizhao12 closed 4 years ago

meizhao12 commented 4 years ago

Hi, I requested our school computing center to install ASAP. However, they failed to install it. Below is what they reported.

Following instructions given at

https://github.com/oschwengers/asap#docker

I was trying to build ASA3P singularity container (asa3p.simg) from its docker image hosted at

https://hub.docker.com/r/oschwengers/asap/

The following is the command I used:

singularity build asa3p.simg docker://oschwengers/asap

asa3p.simg was generated. However, ASA3P core scripts were not generated successfully in asa3p.simg. Its asap/asap-docker.sh script can not be found in its container.

oschwengers commented 4 years ago

Hi @meizhao12 and thanks for reaching out. So far I do not have any experience with an ASA³P singularity image derived from the Docker image. I haven't tested it yet but I guess there might be some issues as ASA³P is using a Singularity container itself in its Docker container. But feel free to play around and feed back your findings.

Regarding the asap-docker.sh script: This is not included within the Docker image. It is included in the asap volume (asap.tar.gz). Just download and extract the tarball and then execute the shell script. It will itself start the Docker container.

Please, let me know if I I could clarify your issues a little bit. If not, please do not hesitate to keep asking.

oschwengers commented 4 years ago

I'll close this issue. If the issue remains or there are unanswered questions, please feel free to reopen this.