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clemgoub / dnaPipeTE

dnaPipeTE (for de-novo assembly & annotation Pipeline for Transposable Elements), is a pipeline designed to find, annotate and quantify Transposable Elements in small samples of NGS datasets. It is very useful to quantify the proportion of TEs in newly sequenced genomes since it does not require genome assembly and works on small datasets (< 1X).
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Update RepeatMasker libraries with RepBase #68

Closed sigau closed 2 years ago

sigau commented 2 years ago

Hi! I installed your program using the singularity img and I try to update the RepeatMasker libraries with the RepBase library I have. So I follow what was said in the issue #46, putting my Repbase Dfam.h5 in /opt/dnaPipeTE/bin/RepeatMasker/Libraries, but there is no RepeatMasker in bin. I find it in /opt/RepeatMasker/Libraries/ but hen I try to cp my Dfam.h5 in Libraries/ I got the error : cp: cannot create regular file '/opt/RepeatMasker/Libraries/Dfam.h5': Read-only file system

I try to chmod the folder, but I got the same error : chmod: changing permissions of '/opt/RepeatMasker/Libraries/Dfam.h5': Read-only file system

Is there another way of using RepBase with dnaPipeTE ?

Thanks so much for any help! Gautier

clemgoub commented 2 years ago

Dear Gautier,

Indeed the best way would be to re-build the docker container from which the singularity is built, including Repbase. Unfortunately, due to licensing I cannot distribute Repbase. I will however update it with the latest Dfam ASAP.

You can modify the Dockerfile (and associated script dockerinit.sh) in order to re-build the container with Docker (you can further convert it to a Singularity image).

In the meantime, the best/simple option would be to convert your Repbase into a fasta file which you can use externally as a library for RepeatMasker. You can use a custom fasta library with dnaPipeTE with the option -RM_lib <file.fasta>

Thanks for pointing that out and let me know if you need further help!

Best,

Clément

sigau commented 2 years ago

Hi ! So I update the RepeatMasker libraries without modifying the dockerfile/initdocker.sh by following the method from dfam github ( https://github.com/Dfam-consortium/TETools). I put it there if it can be useful for other users :

It should work on singularity and docker :

Then you should have a new RepeatMaskerLib.h5 with your update libraires

Anyway thank you Clement for your help and for the pipeline,

Best,

Gautier

clemgoub commented 2 years ago

Hello and thank you Gautier for sharing your solution here!