astrazeneca / detectis Goto Github PK

Hi there,

I have a problem creating the Singularity container. The apt-get installation process waits for user input on postfix configuration, but the user input is not accepted (see below). When adding the dialog package to the list of packages in detectIS.rec, a configuration dialog will be shown on console, but there is no option to select.

Preparing to unpack .../205-postfix_3.3.0-1ubuntu0.4_amd64.deb ...
debconf: unable to initialize frontend: Dialog
debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76.)
debconf: falling back to frontend: Readline
Postfix Configuration
---------------------

Please select the mail server configuration type that best meets your needs.

 No configuration:
  Should be chosen to leave the current configuration unchanged.
 Internet site:
  Mail is sent and received directly using SMTP.
 Internet with smarthost:
  Mail is received directly using SMTP or by running a utility such
  as fetchmail. Outgoing mail is sent using a smarthost.
 Satellite system:
  All mail is sent to another machine, called a 'smarthost', for delivery.
 Local only:
  The only delivered mail is the mail for local users. There is no network.

  1. No configuration  3. Internet with smarthost  5. Local only
  2. Internet Site     4. Satellite system
General type of mail configuration: 1       
1
1

Would it be save to just remove the package mailutils from the package list in detectIS.rec, to avoid that buggy configuration? What limitations are to be expected without that package?

OS: Ubuntu 18.04
conda version : 4.7.12
detectIS: bc08f49 (current master)

Thanks

Greetings and thank you for making this workflow available for others to use.

We've successfully run it, but we'd like to also further visualize the outputs. While the PAF alignment files are available, it would also be useful (in our opinion) to have the workflow return a list of the barcodes that are "matched" between the genome and insert. My Perl is very rusty but I think it would be performed in verify_spreads_is() and verify_split_reads() functions in DetectSpltR.pm? Any suggestions on how to proceed would be appreciated.

Also, do you accept pull requests?

Thanks!