IMP issueshttps://git-r3lab.uni.lu/IMP/IMP/-/issues2018-10-19T15:40:49+02:00https://git-r3lab.uni.lu/IMP/IMP/-/issues/138IMP-specific idba conda recipe needed2018-10-19T15:40:49+02:00Cedric LacznyIMP-specific idba conda recipe needed`idba_ud` **source** code needs to be modified to support long*er* reads.
In the Docker version, this is handled in https://git-r3lab.uni.lu/IMP/IMP/blob/master/docker/Dockerfile-tools#L35.
However, the **bioconda**-based recipe is too...`idba_ud` **source** code needs to be modified to support long*er* reads.
In the Docker version, this is handled in https://git-r3lab.uni.lu/IMP/IMP/blob/master/docker/Dockerfile-tools#L35.
However, the **bioconda**-based recipe is too conservative:
https://github.com/bioconda/bioconda-recipes/blob/fbe3701a7bed202cc83cd4e5652034b703d0d7b0/recipes/idba/idba-kmer.patch#L21
Hence, we would need to create our **own** recipe.Deepti MittalDeepti Mittalhttps://git-r3lab.uni.lu/IMP/IMP/-/issues/126`metaquast` rule: ERROR! Failed downloading SILVA rRNA gene database2018-10-19T15:42:47+02:00Fredrik Boulund`metaquast` rule: ERROR! Failed downloading SILVA rRNA gene databaseHi, just encountered this message in my output from the `metaquast` rule. It seems everything continues anyway, but I couldn't find any other mention of this warning message in any other issues so far, so figured I'd report it anyway.
`...Hi, just encountered this message in my output from the `metaquast` rule. It seems everything continues anyway, but I couldn't find any other mention of this warning message in any other issues so far, so figured I'd report it anyway.
```
Downloading SILVA ribosomal RNA gene database...
ERROR! Failed downloading SILVA rRNA gene database (http://www.arb-silva.de/fileadmin/silva_databases/release_119/Exports/SILVA_119_SSURef_Nr9_tax_silva.fasta.gz)! The search for reference genomes cannot be performed. Try to download it manually in /home/imp/lib/quast-release_3.1/lbs/blast/16S_RNA_blastdb and restart MetaQUAST.
NOTICE: No references are provided, starting regular QUAST with MetaGeneMark gene finder
```Deepti MittalDeepti Mittal