Hello and thanks for this notice of your new release.
I have mostly completed the packaging for sprai, but I have some
questions and comments. I'm sorry that this message is a bit long.
* A question: Is it possible to call ezez* -ec_only without passing the
Celera assembler spec file or even not having Celera assembler
installed? While testing the package, I tried doing so and got an error
about the ca_path being set the nonexistent path
/home/imai/...../wgs-7.8/Linux-amd64/bin, when I had actually deleted
the ca_path configuration line from the ec.spec file I passed in. It
would be nice to do so and be able to use sprai with another assembler
like Falcon.
* As you may know, wgs-assembler has been discontinued and the successor
project is canu [3]. As a result, we are preferring to include canu into
Debian. This makes it more important for the -ec_only mode to be working
without wgs-assembler installed if possible.
* Many of your scripts expose the implementation language in the file
name. Adding language suffixes to executable program names is frowned
upon in Debian[1]. For the Debian package, I'll be making symlinks to
allow the main programs to be called with or without the .pl suffixes.
* Your example [2] shows that only ezez_vx1.pl. ezez4qsub_vx1.pl, and
fa2fq.pl are called directly by the user, while the package installs
many other programs. I intend to make the package install ezez* to
/usr/bin and place the remaining programs in /usr/lib/sprai. I will
patch the ezez* scripts so that the sprai_path is defined as such.
* I personally recommend adding a changelog to your source distribution.
It helps with determining the urgency of upgrading and keeping track of
when particular features were added. The latter helps to be able to
specify minimum version requirements in a project, for example.
Many thanks and regards
Afif
1.https://wiki.debian.org/UpstreamGuide#Language_extensions_in_scripts
2.http://zombie.cb.k.u-tokyo.ac.jp/sprai/Example.html
3.http://canu.readthedocs.org/en/stable/
على الأربعاء 13 نيسـان 2016 18:59، كتب Takamasa Imai:
>Dear Afif,
>
>Sprai version 0.9.9.13 was released.
>Please usehttp://zombie.cb.k.u-tokyo.ac.jp/sprai/dist/sprai-0.9.9.13.tar.gz .
>This version uses less memory.
>
-- Afif Elghraoui | عفيف الغراوي http://afif.ghraoui.name