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Message when passed non-valid path to bowtie2 #33

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StevenWingett opened this issue Oct 22, 2020 · 0 comments
Open

Message when passed non-valid path to bowtie2 #33

StevenWingett opened this issue Oct 22, 2020 · 0 comments
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Could do better Not actually a bug per se, but a fix is required here to make the program more elegant

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@StevenWingett
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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

@StevenWingett StevenWingett added the Could do better Not actually a bug per se, but a fix is required here to make the program more elegant label Oct 22, 2020
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Labels
Could do better Not actually a bug per se, but a fix is required here to make the program more elegant
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