[Debian-med-packaging] Bug#623558: biomaj: Location of pid file

[Anthony Boureux]

Package: biomaj
Version: 1.1.0-1
Severity: minor

No problem during install and running the sample alu db.
But, I got a minor error

/usr/share/biomaj/bin/biomaj.sh: line 103: /usr/share/biomaj/tmp/.bmajpid_alu:
Aucun fichier ou dossier de ce type (for no french speaker => means no found or
directory found)

In fact /usr/share/biomaj/tmp doesn't exist, and I think is ok with the debian
policy.

The code in biomaj.sh is :
echo $$>$BIOMAJ_ROOT/tmp/.bmajpid_$arg

with $BIOMAJ_ROOT = /usr/share/biomaj

There is a tmp directory for biomaj (tmp.dir in /etc/biomaj/general.conf) but
it's use by the java code not the shell script starting biomaj.

I think that the pid file should go to /var/lib/biomaj/tmp or /var/run/biomaj
or either /tmp
/var/lib/biomaj/tmp is created by the package so it can be use, even if you
change the location in general.conf (like I did, to put databases on another
partition).

Thanks for the packaging.

Best regard,
Anthony.



-- System Information:
Debian Release: wheezy/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: i386 (i686)

Kernel: Linux 2.6.38-2-686-bigmem (SMP w/1 CPU core)
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/bash

Versions of packages biomaj depends on:
ii  ant                1.8.0-4               Java based build tool like make
ii  ant-contrib        1.0~b3+svn177-2       collection of tasks, types and oth
ii  debconf [debconf-2 1.5.38                Debian configuration management sy
ii  junit4             4.8.2-2               JUnit regression test framework fo
ii  libcommons-dbcp-ja 1.4-1                 Database Connection Pooling Servic
ii  libcommons-net-jav 1.4.1-2               internet protocol suite Java libra
ii  libcommons-pool-ja 1.5.6-1               pooling implementation for Java ob
ii  libgnujaf-java     1.1.1-5               free implementation of the javabea
ii  libgnumail-java    1.1.2-5               free implementation of the javamai
ii  libhsqldb-java     1.8.0.10-9            Java SQL database engine
ii  libjcommon-java    1.0.16-1              General Purpose library for Java
ii  libjdom1-java      1.1.1+dfsg-1          lightweight and fast library using
ii  libjfreechart-java 1.0.13-3              Chart library for Java
ii  libjgoodies-forms- 1.3.0-1               Framework to lay out and implement
ii  libjsch-java       0.1.42-2              pure Java implementation of the SS
ii  liblog4j1.2-java   1.2.15-11             Logging library for java
ii  libmysql-java      5.1.10+dfsg-2         Java database (JDBC) driver for My
ii  liboro-java        2.0.8a-7              Regular expression library for Jav
ii  libregexp-java     1.5-2                 Regular expression library for Jav
ii  libsaxonb-java     9.0.0.4+svn20080322-3 The Saxon-B XSLT Processor
ii  openjdk-6-jdk      6b18-1.8.7-2          OpenJDK Development Kit (JDK)

biomaj recommends no packages.

Versions of packages biomaj suggests:
ii  blast2               1:2.2.24.20100808-2 Basic Local Alignment Search Tool
pn  mysql-community-serv <none>              (no description available)
ii  ncbi-tools-bin       6.1.20100808-2      NCBI libraries for biology applica

-- Configuration Files:
/etc/biomaj/db_properties/global.properties changed [not included]
/etc/biomaj/general.conf changed [not included]

-- debconf information excluded