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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Question: Dependency list is different for install versus documentation #1013

Open benyoung93 opened 3 months ago

benyoung93 commented 3 months ago

Hi @nextgenusfs

This is more a query, and not a problem. Just wanted to get that out there right away 😅

I have used funannotate many times, and I am installing onto a new HPC for the new lab I am in (actually for fungal genomes now woooooooo !!!). Using mamba and conda install.

My install so far with mamba, and then set all the enviro variables, and also eggnog and genemark 

mamba create -n funannotate_env -c conda-forge -c bioconda "python>=3.6,<3.9" funannotate

In the documents the dependency section, the external dependencies say this 

Checking external dependencies...
RepeatMasker: RepeatMasker 4.0.7
RepeatModeler: RepeatModeler 1.0.11
Trinity: 2.5.1
augustus: 3.2.1
bamtools: bamtools 2.4.0
bedtools: bedtools v2.27.1
blat: BLAT v35
diamond: diamond 0.9.19
emapper.py: emapper-1.0.3
ete3: 3.1.1
exonerate: exonerate 2.4.0
fasta: no way to determine
gmap: 2017-06-20
gmes_petap.pl: 4.30
hisat2: 2.1.0
hmmscan: HMMER 3.1b2 (February 2015)
hmmsearch: HMMER 3.1b2 (February 2015)
java: 1.8.0_92
kallisto: 0.43.1
mafft: v7.313 (2017/Nov/15)
makeblastdb: makeblastdb 2.7.1+
minimap2: 2.10-r761
nucmer: 3.1
pslCDnaFilter: no way to determine
rmblastn: rmblastn 2.2.27+
samtools: samtools 1.8
tRNAscan-SE: 1.23 (April 2002)
tbl2asn: unknown, likely 25.3
tblastn: tblastn 2.7.1+
trimal: trimAl v1.4.rev15 build[2013-12-17]
All 30 external dependencies are installed

But on my install, and running the check I only get the following for external dependencies (obvs I havent done signalp yet). 

Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: augustus: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory
bamtools: bamtools 2.5.1
bedtools: bedtools v2.31.1
blat: BLAT v37x1
diamond: 2.1.8
emapper.py: 2.1.12
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2024-02-22
gmes_petap.pl: 4.71_lic
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 17.0.3-internal
kallisto: 0.46.1
mafft: v7.525 (2024/Mar/13)
makeblastdb: makeblastdb 2.14.1+
minimap2: 2.27-r1193
pigz: 2.8
proteinortho: 6.3.1
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.18
snap: 2006-07-28
stringtie: 2.2.1
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 49
tbl2asn: 25.8
tblastn: tblastn 2.14.1+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
    ERROR: signalp not installed

Questions

nextgenusfs commented 3 months ago

If you pin augustus==3.5.0 that should hopefully fix the Augustus issue.

Yeah, the check is probably old code and not really in-line with the current version (apologies), I have no plans to fix or update though. Repeatmasker/modeler support has been dropped due to changes in the licensing agreement with the underlying database.

benyoung93 commented 3 months ago

Hi @nextgenusfs :)

So I fixed the issue (probably not best practices) by the following but thankyou for the augustus fix as well. May be useful for someone else :). 

mamba clean --all
conda config --set channel_priority flexible
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
mamba create -n funannotate_env funannotate

I am getting another error with biopython (https://github.com/nextgenusfs/funannotate/issues/1000) but see that downgrading works for that. That has fixed my test run so yay.

The conda version (installed yesterday) is still funannotate v1.8.15 and I see the biopython problem is fixed in v1.8.16. So thats all good :).