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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Conda installation issues #255

Closed emmadoughty closed 4 years ago

emmadoughty commented 4 years ago

I'm having trouble getting the full nullarbor pipeline to run to completion with various installation issues arising. I've tried a lot of things, this largely summarises it:

conda create -n nullarbor -c bioconda kraken kraken2 centrifuge conda install -c bioconda -c conda-forge -c defaults -c r nullarbor

Added extra channels in desperation

Kraken etc downloaded and export commands added to bashrc

Generating the run directory, it complained that quicktree was not installed

conda install -c bioconda quicktree

When I ran the pipeline, it complained about the prokka and tbl2asn versions

conda update -c bioconda prokka conda update -c bioconda tbl2asn #Couldn't find update conda install -c bioconda/label/cf201901 tbl2asn #Updated but then nullarbor wouldn't run to generate a run directory conda update -c bioconda nullarbor #Nullarbor then ran but complained about prokka and tbl2asn again

Also had issues with make preview as ref.fa wasn't being generated.

Looking for something 'cleaner', my latest install was with: conda create -n test_null -c bioconda -c conda-forge -c defaults -c r kraken kraken2 centrifuge quicktree prokka tbl2asn nullarbor

I could generate the run directory, dependency check was happy but I think I've got the same issue with tbl2asn again. [11:05:32] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka' -Z \/tmp\/tmp.dNgTbB12Em\/prokka.err -i \/tmp\/tmp.dNgTbB12Em\/prokka.fsa 2> /dev/null make: [Makefile:130: 14442/contigs.gff] Error 2 make: Waiting for unfinished jobs.... nullarbor.log

Any help would be greatly appreciated!

rpetit3 commented 4 years ago

Hi @emmadoughty!

I think you were affected by the expired tbl2asn issue (See https://github.com/tseemann/prokka/issues/453). This was recently fixed in Bioconda (https://github.com/bioconda/bioconda-recipes/pull/20117).

I think if you try creating the environment again it should work for you.

Otherwise you can use the test_null environment you already created and install tbl2asn-forever into it.

conda activate test_null
conda install -c conda-forge -c bioconda tbl2asn-forever

Cheers, Robert

tseemann commented 4 years ago

@rpetit3 is correct. prokka is fixed in conda now. you should not need to add any of those manual conda installs - the nullarbor recipe has them all. it suggests something else is wrong. i think you need to set your channel order correctly: https://bioconda.github.io/user/install.html#set-up-channels