[Debian-med-packaging] Bug#1025278: sra-toolkit: binary sratools installed on PATH

[Carl Suster]

Package: sra-toolkit
Version: 3.0.0+dfsg-1
Severity: wishlist

Dear Maintainer,

sra-toolkit installs a binary /usr/bin/sratools, which is intended to be used
via the symlinks installed by the package (since its behaviour is influenced by
the name of the executable):

    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/fasterq-dump -> sratools
    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/fastq-dump -> sratools
    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/prefetch -> sratools
    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/sam-dump -> sratools
    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/sra-pileup -> sratools
    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/srapath -> sratools
    lrwxrwxrwx 1 root root 8 Nov 14 14:22 /usr/bin/vdb-dump -> sratools

Invoking the executable by its original name does nothing useful:

    $  /usr/bin/sratools
    An error occured: unrecognized tool sratools
    If this continues to happen, please contact the SRA Toolkit at https://trace.ncbi.nlm.nih.gov/Traces/sra/

Perhaps sratools should be installed in a private directory like
/usr/lib/sra-toolkit, leaving only the symlinks in /usr/bin.

Given the absence of man pages for the tools, and not being familiar with them,
this caused me some confusion because it appeared something was broken.

-- System Information:
Debian Release: bookworm/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 6.0.0-4-amd64 (SMP w/4 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages sra-toolkit depends on:
ii  libbz2-1.0     1.0.8-5+b1
ii  libc6          2.36-6
ii  libhdf5-103-1  1.10.8+repack-4
ii  libmagic1      1:5.41-4
ii  libncbi-vdb3   3.0.0+dfsg2-4
ii  libncbi-wvdb2  2.11.2+dfsg-6
ii  libncbi-wvdb3  3.0.0+dfsg2-4
ii  libre2-9       20220601+dfsg-1
ii  libxml2        2.9.14+dfsg-1.1+b2
ii  zlib1g         1:1.2.13.dfsg-1

Versions of packages sra-toolkit recommends:
ii  med-config  3.7.3

sra-toolkit suggests no packages.

-- no debconf information