On 28.07.21 06:30, Andreas Tille wrote:
Hi, On Wed, Jul 28, 2021 at 01:13:38PM +0900, Charles Plessy wrote:I had a quick lookKind regards Andreas. (git grep) at the source code of ArrayExpressHTS and although it has an option to indicate the path to fasta_formatter, it appears to never use it.
I patched it out. Many thanks for spotting that!
... and may be report this issue to ArrayExpressHTS upstream?
With that boost, I also had a look at patching out tophat but it seems like that protocol is much depending on all the bits and pieces that were nice and shiny when the package was introduced in 2010. We should discuss with upstream what to do about the package. At the moment, the only values I see are a) retrieving data from ArrayExpress for RNA-seq data (judge yourselves on https://www.bioconductor.org/packages/release/bioc/vignettes/ArrayExpressHTS/inst/doc/ArrayExpressHTS.R) which was my motivation to package it b) increasing %age of what we cover from Bioconductor c) increasing %age of what we cover from CRAN Best, Steffen