Lev Gorenstein

BRAKER2 hardcodes AUGUSTUS_CONFIG_PATH value

1

Hello Biocontainers team, While working with BRAKER2 singularity image (`singularity pull docker://quay.io/biocontainers/braker2:2.1.6--hdfd78af_3`) the program crashes with an error ``` # Wed Apr 21 21:11:44 2021: ERROR: in file /usr/local/bin/braker.pl at...

MrBayes container needs ssh or rsh installed

4

MrBayes container is missing `ssh` and/or `rsh`. Because of this, the MPI version of the program can not be launched: ``` $ singularity run https://depot.galaxyproject.org/singularity/mrbayes:3.2.7--h19cf415_2 mpirun -np 2 mb-mpi --------------------------------------------------------------------------...

samtools: no Perl in the container, tools fail to run

2

Looks like Samtools containers is missing Perl, so many installed tools fail to run (`blast2sam.pl`, `bowtie2sam.pl`, etc): ``` $ singularity run https://depot.galaxyproject.org/singularity/samtools:1.9--h10a08f8_12 blast2sam.pl WARNING: Skipping mount /var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't...

Missing <linux/kcmp.h> breaks build on CentOS 7

2

Hello, and thank you for the great tool! Reporting a problem with building NVTOP on an HPC cluster here. CentOS 7.9, kernel 3.10.0-1160.62.1.el7.x86_64, CUDA 11.7. Cmake part goes fine, but...

This way the generated Singularity image could also be executed directly (no need for `singularity exec`).

Should module aliases be dereferenced on listing?

7

**Describe the bug** Not a bug per se, more of a question. Currently, if a `module_alias("myalias", "xyz/1.2.3")` is defined, and the user does: ``` module load myalias module list ```...

Relion GUI is not in relion/3.* containers

4

Can not launch the Relion GUI for the 3.* version of the containers: ``` $ module load relion/3.1.0 $ relion INFO legacy OFED driver set: 4.7-3.2.9.0 FATAL Failed to find...

Make all modules export a variable with their image name

2

Something it's very convenient to do a quick `singularity shell` or `singularity exec` with the container - which requires to know where the image is. Having the module define an...

Add '--pid' to the singularity command

5

I noticed that sometimes if the application run is interrupted (e.g. Ctrl-C'd), it leaves behind some of this processes (mpiexec.hydra, or python, etc). I discovered it while playing with a...

Add GAMESS module

2

Please take a look at my attempt to create a module for the [GAMESS container](https://ngc.nvidia.com/catalog/containers/hpc:gamess). Took a bit of sweat because of a very particular input and output locations that...