doctor.py gives errors

[ronish-droid]

I uninstalled and installed it again but received the same errors:

# Doctor! Doctor! Give me the news.
# Checking symptoms ...
# bwa           ... OK
# datamash      --> ERROR
# fastqc -h     --> ERROR
# hisat2        --> ERROR
# featureCounts --> ERROR
# efetch        ... OK
# esearch       ... OK
# samtools      ... OK
# fastq-dump    ... OK
# bowtie2       --> ERROR
# bcftools      --> ERROR
# seqtk         --> ERROR
# seqkit        --> ERROR
# bio           ... OK
# fastq-dump -X 1 -Z SRR1553591 ... OK
#
# Found some problems
#
# Unable to run: datamash, fastqc -h, hisat2, featureCounts, bowtie2, bcftools, seqtk, seqkit
#
# Check the Biostar Handbook for installation help.

[ialbert]

typically, this means that the bioinfo environment is not activated.

make sure that you have activated bash (on MacOS) and that you have opened a new terminal and have activated bioinfo

micromamba activate bioinfo

[ronish-droid]

Thank you!

…

On Sun, 23 Mar 2025 at 14:17 Istvan Albert ***@***.***> wrote: typically, this means that the bioinfo environment is not activated. make sure that you have activated bash (on MacOS) and that you have opened a new terminal and have activated bioinfo micromamba activate bioinfo — Reply to this email directly, view it on GitHub <#347 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BQYYABTLOCPA6N2ILSOBNS32V2Q4RAVCNFSM6AAAAABZS64CHCVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTENJZGIZDANA> . You are receiving this because you authored the thread.Message ID: ***@***.*** com>

[EmediongFrancis]

@ronish-droid, did you fix this? It seems you did not install some of the packages.