I’ve been having issues installing BALDR (https://github.com/BosingerLab/BALDR),
which consists of half a dozen package components and a Perl wrapper.
You previously attempted to compile one of the components (Trinity 2.3.2)
and encountered many errors—the Trinity version is over 5 years old &
the BALDR github stipulates that “Newer versions are not compatible.”
One of the questions I have is that there is a Docker image alternative installation
procedure provided. I have some, but not a lot of, experience with Docker, but would using
their Docker image avoid these compiler issues? In any event, I tried this method
of install, following the github steps listed, but encountered an error during the STAR
genome index generation:
[root@2f4cb214883c STAR_GRCh38]# STAR --runThreadN 4 --runMode genomeGenerate --genomeDir STAR_GRCh38_index --genomeFastaFiles Homo_sapiens.GRCh38.dna.primary_assembly.fa --sjdbGTFfile Homo_sapiens.GRCh38.86.gtf --sjdbOverhang 100 Feb 11 02:32:07 ..... started STAR run Feb 11 02:32:07 ... starting to generate Genome files
Killed
The iMac I'm running on has 64GB of memory.
I might be doing something wrong. If I can’t get the Docker approach
to work, then I’m thinking that the next step would be for me to try to
modify the Perl wrapper to work with current versions of
all components. And finally, if that doesn’t work then I’ll
just try to implement my own solution from scratch.
Hi Fitzwit,
I’ve been having issues installing BALDR (https://github.com/BosingerLab/BALDR), which consists of half a dozen package components and a Perl wrapper. You previously attempted to compile one of the components (Trinity 2.3.2) and encountered many errors—the Trinity version is over 5 years old & the BALDR github stipulates that “Newer versions are not compatible.”
One of the questions I have is that there is a Docker image alternative installation procedure provided. I have some, but not a lot of, experience with Docker, but would using their Docker image avoid these compiler issues? In any event, I tried this method of install, following the github steps listed, but encountered an error during the STAR genome index generation:
The iMac I'm running on has 64GB of memory.
I might be doing something wrong. If I can’t get the Docker approach to work, then I’m thinking that the next step would be for me to try to modify the Perl wrapper to work with current versions of all components. And finally, if that doesn’t work then I’ll just try to implement my own solution from scratch.
Any suggestions/advice? Thanks for your time.