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LANL-Bioinformatics / EDGE

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.
https://lanl-bioinformatics.github.io/EDGE/
GNU General Public License v3.0
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Fresh EDGE Install Issues #34

Open loganvoegtly opened 4 years ago

loganvoegtly commented 4 years ago

I have been performing a fresh install of EDGE and have encountered a few issues with the INSTALL.sh and programs failing initial testing. Below are some issues I encountered (listing them in one issue rather than multiple issue tickets):

  1. In INSTALL.sh multiple programs check for version but always fail the check. This can be fixed by making the version number a string.
  2. Installing some software using offline conda packages and then installing other packages from online conda repos take a very long time to resolve dependencies. I would recommend to do all offline install or all online install, not a combination.
  3. Qiime2 had issues with offline install, had to modify INSTALL.sh to install from online.
  4. Antismash has ~1gb database which needs to be downloaded during conda install. Could this be part of the pre-downloaded databases?
  5. Unicycler is not compatible with SPAdes 3.13.x. SPAdes 3.13.x deletes graphs as it completes the K-mer iteration, which are used by unicycler to choose the best starting graph. Recommend using SPAdes 3.12.x.
  6. I would recommend default quality score cutoffs to be Q20 and not Q5.
  7. There is inconsistency on how the status of a job is reported.
  8. It would be convenient to add fastg to apache file for downloading.
  9. Checkm did not properly setRoot when doing install.
  10. Gottcha2 fails to run due to parameters used in EDGE being removed from the program.
kwdavenport commented 4 years ago

Thanks, Logan. We have encountered some of these issues, but not all. We will look into all of them.

Best,

Karen

From: Logan Voegtly notifications@github.com Sent: Thursday, October 24, 2019 8:16 AM To: LANL-Bioinformatics/EDGE Cc: Subscribed Subject: [LANL-Bioinformatics/EDGE] Fresh EDGE Install Issues (#34)

I have been performing a fresh install of EDGE and have encountered a few issues with the INSTALL.sh and programs failing initial testing. Below are some issues I encountered (listing them in one issue rather than multiple issue tickets):

  1. In INSTALL.sh multiple programs check for version but always fail the check. This can be fixed by making the version number a string.
  2. Installing some software using offline conda packages and then installing other packages from online conda repos take a very long time to resolve dependencies. I would recommend to do all offline install or all online install, not a combination.
  3. Qiime2 had issues with offline install, had to modify INSTALL.sh to install from online.
  4. Antismash has ~1gb database which needs to be downloaded during conda install. Could this be part of the pre-downloaded databases?
  5. Unicycler is not compatible with SPAdes 3.13.x. SPAdes 3.13.x deletes graphs as it completes the K-mer iteration, which are used by unicycler to choose the best starting graph. Recommend using SPAdes 3.12.x.
  6. I would recommend default quality score cutoffs to be Q20 and not Q5.
  7. There is inconsistency on how the status of a job is reported.
  8. It would be convenient to add fastg to apache file for downloading.
  9. Checkm did not properly setRoot when doing install.
  10. Gottcha2 fails to run due to parameters used in EDGE being removed from the program.

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