M Bernt
Just stumbled over [shellcheck](https://github.com/koalaman/shellcheck). Would be nice to integrate this in planemo. Could save quite some time if missing double quotes etc are mentioned to the tool author automatically.
the removed test allows the --help and --version flags to work as expected. the change to the shebang lines allow to run the scripts on systems where python/perl is installed...
With the current scater package the following error appears: ``` Error: 'calculateQCMetrics' is defunct. Use 'perCellQCMetrics' instead. ``` https://github.com/LuyiTian/scPipe/blob/a9948cf4287eae6ac1252b84c3625f16f2cff114/inst/extdata/report_template.Rmd#L196
Shouldn't `biomaRt` be loaded automatically in order to use this https://github.com/LuyiTian/scPipe/blob/081979035700f11f8d97a2cebdcd227b84d98f4b/R/biomart_methods.R#L35 ``` Error in useMart("ensembl"): could not find function "useMart" ```
When running `mlocarna` I sometimes get the following error with version 1.9.2.3 ``` /home/berntm/miniconda3/envs/[email protected]/bin/locarna_p: unrecognized option '--width' Cannot compute match probabilities by /home/berntm/miniconda3/envs/[email protected]/bin/locarna_p input/fruA input/fdhA --min-bm-prob=0.0005 --min-am-prob=0.0005 --indel -350 --indel-opening...
Having problems with MPA. Input is a 600MB fasta file and 441MB mgf. Might be a memory problem, but -Xmx 70GB is already quite a lot (actual available memory was...
Dear MPA developers @thilus @tivdnbos, I'm working on the mpa-portable bioconda recipe and wonder if it is possible to replace the precompiled versions of X!Tandem and Comet (and maybe also...
During the execution of SearchGUI I observe the following in the errors: ``` MS-GF+ Release (v2021.01.08) (8 January 2021) Java 11.0.8-internal (N/A) Linux (amd64, version 3.10.0-1160.el7.x86_64) Loading database files... Warning:...
One of the search engines (tide) seems to need glibc: ``` /gpfs1/work/songalax/galaxy-dev/database/jobs_directory/005/5277/working/bin/resources/Tide/linux/linux_64bit/crux: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /gpfs1/work/songalax/galaxy-dev/database/jobs_directory/005/5277/working/bin/resources/Tide/linux/linux_64bit/crux) ``` Unfortunatelly we execute on a cluster system an can...
xref https://github.com/galaxyproject/tools-iuc/issues/3516 ``` Traceback (most recent call last): File "/dep/_conda/envs/[email protected]/lib/python3.6/logging/handlers.py", line 71, in emit if self.shouldRollover(record): File "/dep/_conda/envs/[email protected]/lib/python3.6/logging/handlers.py", line 187, in shouldRollover msg = "%s\n" % self.format(record) File "/dep/_conda/envs/[email protected]/lib/python3.6/logging/init.py", line...