Message when passed non-valid path to bowtie2 #33
Description
The message below could be more elegant:
(base) ultraviolet@ultraviolet-X555QA:~$ fastq_screen_v0.13.0/fastq_screen fsq_test_dataset.fastq.gz
Using fastq_screen v0.13.0
Reading configuration from '/home/ultraviolet/fastq_screen_v0.13.0/fastq_screen.conf'
Aligner (--aligner) not specified, but Bowtie2 path and index files found: mapping with Bowtie2
Using '/usr/local/bin/bowtie2-2.3.3.1-linux-x86_64/bowtie2' as Bowtie 2 path
Adding database Human
Adding database Mouse
Adding database Ecoli
Adding database rRNA
Adding database MT
Adding database Lambda
Adding database Vectors
Adding database Adapters
Use of uninitialized value $path_to_bowtie in string eq at fastq_screen_v0.13.0/fastq_screen line 1515, line 252.
Aligner bowtie2 not exectable at '/usr/local/bin/bowtie2-2.3.3.1-linux-x86_64/bowtie2', please adjust configuration