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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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repbase #20

Closed toto2011 closed 2 years ago

toto2011 commented 5 years ago

it seems giri asks for non-free subscription to obtain the RM libraries so my username and password are only getting some xml file from their repository. any ideas how to solve this? would a flat fasta be enough?

thanks!

clemgoub commented 5 years ago

Hello toto2011,

Indeed RepBase has moved to a subscription-based mode and this impacts the installation of dnaPipeTE.

One quick fix is to obtain the fasta sequence of the RepeatMasker libraries and pass it in the command line with the -RM_lib argument.

The format must be as follow:

>TE_NAME#Class/Subclass with Class/Subclass identical to the list available in the first column of the file new_list_of_RM_superclass_colors_sortedOK Otherwise TE will be classified as "unknown".

I'm looking for a more user friendly solution, but seems that the new rules on Repbase will make it difficult.

Please let me know if you have any trouble,

Clément

clemgoub commented 2 years ago

Closing this issue since it concerns the non-container version. Please DM if further support is needed. Thank you!