Troubles with entrez direct

[ialbert]

Entrez direct tools automatically detect the platforms at runtime.

On Mac M1 processors is possible to end up with a situation where the tool is installed as a Rosetta Unix mode but the terminal is running as ARM 1 or vice-versa.

Reinstall entrez direct with the following command:

yes | sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" > /dev/null

[chuddy-ibk]

I have issues with edirect and since a complete new environment setup also did not work to set up an environment, I try to "repair" the old one where everything else hopefully works.
when i type:
"
$ esearch -db SSR -query SSR1553606 | head
"

following appears:
"
WARNING: FAILURE ( Thu Mar 9 10:25:06 CET 2023 )
nquire -url https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -retmax 0 -usehistory y -db SSR -term SSR1553606 -tool edirect -edirect 16.2 -edirect_os Linux -email chuddy@chuddy-HP-ProBook-470-G5
Invalid db name specified: SSR
SECOND ATTEMPT
WARNING: FAILURE ( Thu Mar 9 10:25:08 CET 2023 )
nquire -url https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -retmax 0 -usehistory y -db SSR -term SSR1553606 -tool edirect -edirect 16.2 -edirect_os Linux -email chuddy@chuddy-HP-ProBook-470-G5
Invalid db name specified: SSR
LAST ATTEMPT
ERROR: FAILURE ( Thu Mar 9 10:25:11 CET 2023 )
nquire -url https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -retmax 0 -usehistory y -db SSR -term SSR1553606 -tool edirect -edirect 16.2 -edirect_os Linux -email chuddy@chuddy-HP-ProBook-470-G5

Invalid db name specified: SSR QUERY FAILURE SSR 1 (bioinfo) "

When I try to use the
"yes | sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)" > /dev/null"
then following appears:

"
tar: Skipping to next header

gzip: edirect.tar.gz: invalid compressed data--format violated
tar: Exiting with failure status due to previous errors

gzip: xtract.Linux.gz: invalid compressed data--format violated
chmod: cannot access 'xtract.Linux': No such file or directory

gzip: rchive.Linux.gz: invalid compressed data--format violated
chmod: cannot access 'rchive.Linux': No such file or directory

gzip: transmute.Linux.gz: invalid compressed data--format violated
chmod: cannot access 'transmute.Linux': No such file or directory
(bioinfo)
"

any suggestions?

[VladimirVinarsky]

Hello I got the following output from the doctor.py, what should I do?
Thank you for your help

$ doctor.py

Doctor! Doctor! Give me the news.

Checking symptoms ...

bwa ... OK

datamash ... OK

fastqc -h ... OK

hisat2 ... OK

seqret -h --> ERROR

featureCounts ... OK

efetch ... OK

esearch ... OK

samtools ... OK

fastq-dump ... OK

bowtie2 ... OK

bcftools ... OK

seqtk ... OK

seqkit ... OK

bio ... OK

fastq-dump -X 1 -Z SRR1553591 ... OK

Found some problems

Unable to run: seqret -h

Check the Biostar Handbook for installation help.

(bioinfo)

[ialbert]

it is unexpected that only that tool failed, but in reality that tool is not needed anymore since we have the bio package, so I would recommend moving on

I will redesign the install to not check for this particular tool: seqret

[VladimirVinarsky]

Thank you:)