Line 1129 fails, when running SAKE due to the hard-coded archive being gone (the page for it leads to "The Ensembl Archive you tried to reach is not available. You can go to one of the other available archives:").
For my run of the tool, I edited the code to
ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", path="/biomart/martservice" ,dataset="hsapiens_gene_ensembl")
Which, I guess, is not ideal for reproducibility, unless latest/default useMart version is recorded separately. However using the older database may also negatively impact the analysis. Would it be possible to just update a code for trying to pull the latest version or give choice to the user, from which archive to pull the database?
Line 1129 fails, when running SAKE due to the hard-coded archive being gone (the page for it leads to "The Ensembl Archive you tried to reach is not available. You can go to one of the other available archives:").
ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="jul2016.archive.ensembl.org", path="/biomart/martservice" ,dataset="hsapiens_gene_ensembl")For my run of the tool, I edited the code to
ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", path="/biomart/martservice" ,dataset="hsapiens_gene_ensembl")Which, I guess, is not ideal for reproducibility, unless latest/default useMart version is recorded separately. However using the older database may also negatively impact the analysis. Would it be possible to just update a code for trying to pull the latest version or give choice to the user, from which archive to pull the database?