~/bin/doctor.py

[nanthony80]

Hi there, I'm trying to run doctor.py to check the installation

~/bin/doctor.py

I get this message:

$ ~/bin/doctor.py

Doctor! Doctor! Give me the news.

Checking symptoms ...

bwa --> ERROR

datamash --> ERROR

fastqc -h --> ERROR

hisat2 --> ERROR

seqret -h --> ERROR

featureCounts --> ERROR

efetch --> ERROR

esearch --> ERROR

samtools --> ERROR

fastq-dump --> ERROR

bowtie2 --> ERROR

bcftools --> ERROR

seqtk --> ERROR

seqkit --> ERROR

bio --> ERROR

fastq-dump -X 1 -Z SRR1553591 --> ERROR

Found some problems

Unable to run: bwa, datamash, fastqc -h, hisat2, seqret -h, featureCounts, efetch, esearch, samtools, fastq-dump, bowtie2, bcftools, seqtk, seqkit, bio, fastq-dump -X 1 -Z SRR1553591

Check the Biostar Handbook for installation help.

(base)

Any suggestions on how to fix this to step 12 "turn off the nag messages by parallel" in the step-by-step installation guide?

[nanthony80]

The issue is solved. After being unable to do the quick install and trying unsuccessfully to do the step-by-step install, I was able to get the quick install to work by using:

curl http://data.biostarhandbook.com/uninstall.sh | bash
(found in this thread #228)

then running this again:

curl http://data.biostarhandbook.com/install.sh | bash