[Debian-med-packaging] Bug#834864: hisat2: FTBFS on kfreebsd-amd64: help2man: can't get `--help' info from ./hisat2

[Steven Chamberlain]

Tags: 834864 + patch
User: debian-bsd at lists.debian.org
Usertags: kfreebsd

Hello,

The hisat2 binary actually had this problem on kfreebsd:

| $ ./hisat2
| (ERR): Expected hisat2 to be in same directory with hisat-align:
| /build/hisat2-2.0.4/
| Exiting now ...

which happens because it looks for a different filename, when the OS is
not "linux" or "darwin".

Please see the attached patch to correctly recognise *freebsd platforms.
It fixes the hisat2 binary and the Debian package build.

(Though I might suggest to upstream, that they change the test to
"os_is_windows" and use the ordinary filename otherwise).

Thanks!
Regards,
-- 
Steven Chamberlain
steven at pyro.eu.org
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Date: Sun, 21 Aug 2016 21:32:59 +0100
From: Steven Chamberlain <stevenc at debian.org>
Subject: Identify *freebsd as a UNIX-like OS

Match "gnukfreebsd" or "freebsd", when assigning $os_is_nix.

--- a/hisat2
+++ b/hisat2
@@ -45,7 +45,7 @@
 
 ($vol,$script_path,$prog) 
                 = File::Spec->splitpath($prog);
-my $os_is_nix   = ($^O eq "linux") || ($^O eq "darwin");
+my $os_is_nix   = ($^O eq "linux") || ($^O eq "darwin") || ($^O =~ /freebsd$/);
 my $align_bin_s = $os_is_nix ? 'hisat2-align-s' : 'hisat2-align-s.exe'; 
 my $build_bin   = $os_is_nix ? 'hisat2-build' : 'hisat2-build.exe';               
 my $align_bin_l = $os_is_nix ? 'hisat2-align-l' : 'hisat2-align-l.exe'; 
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