singularity issue

[Spieler2999]

I am trying to get GraffiTE installed on our server, but I am having some issues with singularity. I am not sure if this is on my side and I need to update something? I can clone the github repository and all files are downloaded. When I then do the second step I get an error:

singularity pull --arch amd64 graffite_latest.sif library://cgroza/collection/graffite:latest

FATAL: Unable to get library client configuration: remote has no library client (see https://apptainer.org/docs/user/latest/endpoint.html#no-default-remote)

[cgroza]

Hello,

I just ran the same command on our server and it works. It appears to be due to a difference in the configuration of singularity (now apptainer). Could you include the singularity version you are using?

It is possible that your singularity installation is configured with no default remote server from which to pull images.

[cgroza]

We did some research, and it's related to some new defaults in the latest Apptainer/Singularity versions.

Please run these two commands before trying to pull the image:

apptainer remote add --no-login SylabsCloud cloud.sycloud.io
apptainer remote use SylabsCloud
apptainer pull --arch amd64 graffite_latest.sif library://cgroza/collection/graffite:latest

Thank you for bringing these new changes to our attention, we are updating our documentation.

Please see here for a video tutorial: https://hsf-training.github.io/hsf-training-singularity-webpage/02-running-containers/index.html

[Spieler2999]

Hi, Many thanks for fixing the problem so fast!

I could run it with the test data that was provided (see command below). I get 3 folders as output:1_SV_search 2_Repeat_Filtering 3_TSD_search

However, when I change the --genotype false to --genotype true, to get the 4th genotype folder then I get an error:

No such file: /home/mnilsson/GraffiTE/reads.fq -- Check script 'main.nf' at line: 390 or see '.nextflow.log' file for more details

Not sure what I need to change to do the genotyping with the test data?

NXF_VER=20.10.0 nextflow run /home/mnilsson/GraffiTE/main.nf --assemblies /home/mnilsson/GraffiTE/test/GraffiTE_testset/assemblies.csv --reference /home/mnilsson/GraffiTE/test/GraffiTE_testset/hs37d5.chr22.fa --TE_library /home/mnilsson/GraffiTE/test/GraffiTE_testset/human_DFAM3.6.fasta --out testFolder --mammal --genotype false --cpu 2 -with-singularity /home/mnilsson/GraffiTE/graffite_latest.sif

[clemgoub]

Hello!

I'm happy Cristian's fix worked well! Perfect! Now let's see this next issue =)

I think you simply need to add the read input table with --reads <read_input_table.csv>. In the current command, only the assemblies are provided for SV search, but no --reads are present for genotyping.

Also, but this is not critical: when genotyping you don't need to specify --genotype true, it will do it by default. However, the read input table is needed.

NXF_VER=20.10.0 nextflow run /home/mnilsson/GraffiTE/main.nf
--assemblies /home/mnilsson/GraffiTE/test/GraffiTE_testset/assemblies.csv
--reference /home/mnilsson/GraffiTE/test/GraffiTE_testset/hs37d5.chr22.fa
--TE_library /home/mnilsson/GraffiTE/test/GraffiTE_testset/human_DFAM3.6.fasta
--reads /home/mnilsson/GraffiTE/test/GraffiTE_testset/reads.csv
--out testFolder
--mammal
--cpu 2
-with-singularity /home/mnilsson/GraffiTE/graffite_latest.sif

One last thing: Cristian updated the repos yesterday, and normally, the flag NXF_VER=20.10.0 is not needed anymore (make sure you pull the repos before). Let us know if that works =)

[Spieler2999]

Hi, I added the --reads reads.csv and it worked without problems.

I installed GraffiTE again (29.06.2023) and this time I could run without the NXF_VER=20.10.0.

So the installation and test data is running exactly as it should. I will now try with my own data :)

Many thanks!

[clemgoub]

Fantastic! 🎉