genomepy
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vanheeringen-lab
genes and genomes at your fingertips
On some installs `genomepy annotation` fails: ``` gtfToGenePred: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory ``` This is likely an error...
Is there a way of installing genomes from a local file rather than from a URL? In this case the command would be something like genomepy install -p localfile /path/to/local/directory/genomefile.fa.gz
Hi It seems that our firewall prevents accessing the external databases, see errors below. Please what is the IP or hostname and ports numbers of the external databases? we need...
```bash raise ConnectionError(err, request=request) requests.exceptions.ConnectionError: ('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',)) ``` When I use the code with `genomepy search zebrafish`, I got this error How can I...
Hi, thanks for developing such useful tools. just a little suggestion on formatting. [Rich](https://github.com/willmcgugan/rich) can be used to help with formatting things like colorful output, tables, and progress bar. Its...
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Indexing all 100+ versions would be super slow, heavy and prone to errors due to connection stability. Alternatively, we could only index it for genomes ending with `.p*` (e.g. GRCh38.p12)....
Is there a way to specify chromosome order when installing a genome? E.g., when downloading a human genome I want the chromosomes to be sorted in the "normal" way aschr1,...
Hi genomepy team, First, I want to say thanks for this software. Second, I have a question related to the `genome install` command - is there a way to install...
hi! Many thanks for writing this amazing library!! One issue that personally prevents my lab from switching to genomepy is that it seems to store genomes in uncompressed .fa files....
