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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
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Dockerfile compatibility issues with various algorithms, failing to build #105

Closed yutuyt01 closed 2 months ago

yutuyt01 commented 2 months ago

The Dockerfiles for various algorithms fail to build - the error logs are provided below. These are caused by various issues, the most common being the stretch-updates releases being moved to archive.debian.org.

For SCRIBE (stretch releases archived)

E: The repository 'http://deb.debian.org/debian stretch Release' does no longer have a Release file.
E: The repository 'http://deb.debian.org/debian stretch-updates Release' does no longer have a Release file.
E: The repository 'http://security.debian.org/debian-security stretch/updates Release' does no longer have a Release file.

For SCSGL (no such requirements.txt exists in the repository under a scSGL dir?)

ERROR: Could not open requirements file: [Errno 2] No such file or directory: '/scSGL/requirements.txt'

For SINGE: (stretch releases archived)

E: The repository 'http://security.debian.org stretch/updates Release' does no longer have a Release file.
E: The repository 'http://deb.debian.org/debian stretch Release' does no longer have a Release file.
E: The repository 'http://deb.debian.org/debian stretch-updates Release' does no longer have a Release file.

For SINCERITIES: (MRAN is no more as of 2023):

Loading required package: versions
Error in download.file(url, file, quiet = TRUE) :
cannot open URL 'https://mran.revolutionanalytics.com/snapshot'
Calls: install.versions ... sprintf -> latest.MRAN -> scrape.index.dates -> url.lines
Execution halted

There were other issues with other algorithms, but Yiqi has provided updated Dockerfiles for those and they build correctly.

I will make a branch with changes for all but SCSGL, as I do not know of what dependencies the scSGL image needs.

Similar to #99.