Could not find 'trimmomatic'

[MARS2280]

Hi Mr. tseemann

When I try to check the program. The prompt say:

[19:02:25] ERROR: Could not find 'trimmomatic'. Please install it and ensure it is in the PATH.

Now, I downloaded trimmomatic-0.38 and created links in /usr/local/bin or /usr/bin.

What am I doing wrong?

Thanks in advance!

[tseemann]

Do you have a wrapper script called trimmomatic or did you just copy the .jar file?

You need a wrapper script, like that which bioconda or homebrew install.

[MARS2280]

I have a trimmomatic.jar file.

I going to find it in bioconda.

Ok, thanks a lot!

El mar., 10 jul. 2018 a las 19:11, Torsten Seemann (< notifications@github.com>) escribió:

Do you have a wrapper script called trimmomatic or did you just copy the .jar file?

You need a wrapper script, like that which bioconda or homebrew install.

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[Munnj90]

Hi all,

I've got the same issues:

ubuntu@munnj90:~$ sudo ./nullarbor/bin/nullarbor.pl --check [10:53:19] Hello root [10:53:19] This is nullarbor.pl 2.0.20181010 [10:53:19] Send complaints to Torsten Seemann [10:53:20] Found Perl module: Bio::SeqIO [10:53:20] Found Perl module: Cwd [10:53:20] Found Perl module: Sys::Hostname [10:53:20] Found Perl module: Time::Piece [10:53:20] Found Perl module: List::Util [10:53:20] Found Perl module: YAML::Tiny [10:53:20] Found Perl module: Moo [10:53:20] Found Perl module: Path::Tiny [10:53:20] Found Perl module: File::Copy [10:53:20] Found Perl module: File::Spec [10:53:20] Found Perl module: File::Path [10:53:20] Found Perl module: Data::Dumper [10:53:20] Found Perl module: Term::ANSIColor [10:53:20] Found Perl module: SVG [10:53:20] Found Perl module: Text::CSV [10:53:20] Found Perl module: List::MoreUtils [10:53:20] Found Perl module: IO::File [10:53:20] Found 'head' => /usr/bin/head [10:53:20] Found 'cat' => /bin/cat [10:53:20] Found 'install' => /usr/bin/install [10:53:20] Found 'env' => /usr/bin/env [10:53:20] Found 'nl' => /usr/bin/nl [10:53:20] Found 'grep' => /bin/grep [10:53:20] Found 'touch' => /usr/bin/touch [10:53:20] Found 'seqtk' => /usr/bin/seqtk [10:53:20] ERROR: Could not find 'trimmomatic'. Please install it and ensure it is in the PATH. ubuntu@munnj90:~$ trimmomatic Usage: PE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] [-validatePairs] [-basein | ] [-baseout | ] ... or: SE [-version] [-threads ] [-phred33|-phred64] [-trimlog ] [-summary ] [-quiet] ... or: -version ``

I installed trimmomatic with homebrew and its in my path.

Any advice would be appreciated!

Best wishes, John.