Alternative to mget and lfpt

Hi Sarah,

I think there are several answers to your problem:

regarding installation rights, it's not only lftp and wget (I suppose that's what you meant, mget being a command within lftp) that need to be installed, and you may face a lot of trouble setting-up Pantagruel without the admin rights. The solution to this would before us to finally release our (extremely belated) Docker image (see #11 ) that would allow you to run the software without having to install anything (else than the Docker client and that particular image).
regarding the use of lftp and wget : as these tools rely on connecting to the internet to fetch the data, there might be restrictions set in your sever on outgoing port access. In that respect, there is little I can do as if your server has restricted port access any other software would face the same issue. A solution is to download yourself the data and copy them on to the server in the dedicated folders, in which case the download steps during task 00 will be skipped. Options -a, -A and -T allow you to provide your own input data for assemblies and taxonomy, respectively. I believe the only other steps that requires internet access are during tasks 03 and 04 to download the UniProt speclist file and to check the Interproscan last version, respectively. Task 03 uses the command wget http://www.uniprot.org/docs/speclist, but again only if the file is not already present, so you can download it yourself into the folder 03.database/. And I just made a change (7c67acd) to the task 03 script so that the absence of that file is not an issue. Similarly I made a change to the task 04 script so it does not fail if the version check fails (0c381ad). So in summary now you can use Pantagruel without having lftp or wget installed.

Please let me know if you have further troubles.

Best regards, Florent

flass / pantagruel

Alternative to mget and lfpt #22