search

qmarcou / IGoR

IGoR is a C++ software designed to infer V(D)J recombination related processes from sequencing data. Find full documentation at:
https://qmarcou.github.io/IGoR/
GNU General Public License v3.0
47 stars 25 forks source link

Failed to create the man page - where is README.md? #14

Closed smoe closed 6 years ago

smoe commented 6 years ago

Hello,

The installation fails when igor.1, the man page, is not available. After a glimpse at autogen.sh I understand that this is autocreated with pandoc from the README.md, but somehow I fail to locate the README.md file. I tried using README.adoc, instead, but that bails out with too many errors, so I may conclude that there is a file missing from the archive? But then again the build_release script has a comment on README.md but then modifies README.adoc, which kind of indicates that the two are the same file. Sigh. I personally would not mind to see igor.1 distributed directly, so I must admit.

I spotted this issue while preparing a Debian package for IGoR and hope this package to be in your interest. When there are other tools for immune repertoire interpretation that you would like to become part of the distribution then please kindly tell me. MIXCR and changeo are next. A (partial) overview of biological software already shipping with Debian and its derivative distributions is listed on https://blends.debian.org/med/tasks/bio.

Many thanks and regards,

Steffen

qmarcou commented 6 years ago

Hi Steffen, Sorry about this issue it appeared upon transitioning documentation format from Markdown to asciidoc. It has been referred in issue #10, and has already been fixed on the dev branch. The fix will be available on master soon (I apologize for the inconvenience this is forced on me by github not correctly supporting multiffile asciidoc documentation)

Thank you for helping making IGoR more available! Out of curiosity: does this mean IGoR (and the other softwares) will then be available through a packet manager? How will you deal with new versions? Do you have an automated building scheme or do you maintain it by hand ?

Again thank you for your help, Best Quentin

smoe commented 6 years ago

Hi Quentin,

Ah! Sorry, I could have been a bit more investigative about the .adoc format. So, thank you for the opportunity to educate myself on this. For the sake of consistency I will now not fiddle around but wait for your next release.

Concerning updates, it would be darn cool if uploads to Debian could be performed in an automated manner when you tag the next release. For security reasons this does not happen. But let us see how the community develops. For now, should I miss an update of yours, please send me a reminder per eMail. We team-maintain the bio packages in Debian on https://salsa.debian.org/med-team/igor, you can have an account to improve whatever wording or so you find improvable.

That said, I read somewhere that you are using Debian. You are hence cordially invited to upload new versions yourself - all that is missing is a GPG key of yours that is signed by two individuals who have upload permissions already to establish a chain of trust. You find individuals here https://wiki.debian.org/Keysigning/Offers or while conferencing.

The package is on its way to the distribution. The FTPmasters have a manual check on this first upload, which delays it all a bit over the summer time. I'll send a ping once it has arrived.

Cheers,

Steffen

qmarcou commented 6 years ago

Hi Steffen, Better late than ever, this is just to notify you that v1.3.0 has just been released and it should contain quite a few fixes that should ease your work! I'll add a note on this new installation option in the documentation! I'm indeed a debian user, I'll try and investigate these upload requirements! I'll close this issue as I think the initial problem with README.md has been solved Thanks! Quentin