Eric Deveaud

anvi-setup-pfams does not handle already downloaded local file

1

## Short description of the problem despite the `anvi-setup-pfams` help says ```This program by default attempts to use previously downloaded files in your Pfam data directory if there are any.```...

anvi-self-test --suite metagenomics-full :: failure on error

3

Hello anvio-v7 `anvi-self-test --suite metagenomics-full` fails on error/ ``` anvi-self-test --suite metagenomics-full --no-interactive ... SNIP ... GENE LEVEL COVERAGE STATS STORED =============================================== Mode .........................................: STANDARD Num genes ....................................: 23 Num...

db_sort killed :: out of memory

4

Hello, I just installed krakenuniq v0.5.3 and tried to build archea database but I have the following problem. after downloading the taxo and refseq/archea data krakenuniq-build exit with error ```...

bioperl version comparaison :: problem.

1

Hello FYI I noticed that prokka biperl deection is no correct you expect `minbpver = "1.006002"` my bioperl versin claims to be `1.7.8` so `err("Please install BioPerl $minbpver or higher")...

lsd2 not check-ed out

1

Hello, according to #130 and more specifically https://github.com/Cibiv/IQ-TREE/issues/130#issuecomment-619299869 lsd2 should be checked out using the follwoing ``` git clone --recursive https://github.com/Cibiv/IQ-TREE.git cd IQ-TREE git checkout latest git submodule update ```...

Hello, as title says, please embed lsd2 code in archive or document wich version of lsd2 should be used. I know that git clone --recursive, git submodule update and so...

rpath incompatible with LD_LIBRARY_PATH export

15

Hello, after installing goolf-1.7.20 toolchain using --rpath support I was surprised to notice that generated modulefiles for the tools in toolchain still export LD_LIBRARY_PATH. eg: ``` bigmess:~ > module list...

module library reload :: correct way to handle different concurent library version

10

context: we are currently testing//POCing easybuild as our install framework in order to provide scientific softwares to our user. installing BLAST+ and ABYSS using the same toolchain: goolf-1.4.10.eb they were...

amrfinder_update does NOT respect DEFAULT_DB_DIR while amrfinder -u does

11

Hello, `amrfinder_update` does not respect `DEFAULT_DB_DIR` when build with `make DEFAULT_DB_DIR=somewhere` while `amrfinder -u` as it calls `exec (fullProg ("amrfinder_update") + " -d " + shellQuote (dbDir. getParent ()) +...

spades-3.11.0 :: config.info included *.info files not found.

10

Hello while running SPAdes-3.11.0 one of our users reported the following problem. ``` spades.py --meta -1 file1.fastq -2 file.fastq -o test/ -t 4 ``` ends with the following error ```...