Container builders for NCBI Utilities
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Hi,
I've been using your image in my flask app for a while now, so thanks for making that possible! When I try to build from your ncbi/blast/2.13.0 image on docker hub, however, I suddenly get:
GPG error: https://packages.cloud.google.com/apt cloud-sdk-buster InRelease: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY B53DC80D13EDEF05
whereas the same thing worked when my colleague built from this repo instead, so perhaps you need to update the docker hub image?
/ M
When using the Dockerfile to build a container with edirect version 15.0 downloading and integration of the gzipped binaries of transmute, rchive & xtract fails in edirect/setup.sh. Therefore the binaries are missing in the image.
In addition, nquire in the resulting image will not work for URLs with https/TLS. That means that nquire is not able to query the eutils which renders the edirect tools mostly non-functional.
I suspect that the malfunctioning of nquire is also the cause of transmute, rchive & xtract not being integrated into the image.
Example:
docker run --rm -it edirect esearch -db pubmed -query "systematic review[ti]"
curl: (60) SSL certificate problem: unable to get local issuer certificate
More details here: https://curl.haxx.se/docs/sslcerts.html
curl failed to verify the legitimacy of the server and therefore could not
establish a secure connection to it. To learn more about this situation and
how to fix it, please visit the web page mentioned above.
ERROR:
curl command failed ( Thu May 6 18:04:37 UTC 2021 ) with: 60
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi -d retmax=0&usehistory=y&db=pubmed&term=systematic%20review%5Bti%5D&tool=edirect&edirect=15.0&edirect_os=Linux&email=root%40a73e729c6207
WARNING:
FAILURE ( Thu May 6 18:04:36 UTC 2021 )
nquire -url https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ esearch.fcgi -retmax 0 -usehistory y -db pubmed -term "systematic review[ti]" -tool edirect -edirect 15.0 -edirect_os Linux -email root@a73e729c6207
EMPTY RESULT
SECOND ATTEMPT
[...]
The Edirect image is very outdated by now. Are there any plans to update the image?
I can't see why the google-cloud-sdk is in the container.
It is over half the size of the image.
The google-cloud-sdk is over 880 Megabytes.
Hi,
I met this above error when I was doing docker run ncbi/blast.
my docker version is 1.7.0.
Any idea what is going wrong?
Thank you.
Chen
docker.io/ncbi/blast-static:2.15.0 images haven't been built yet:
https://hub.docker.com/r/ncbi/blast-static/tags
Hello,
I'm trying to run magicblast from the docker image, but I'm getting a certification verification issue.
โ docker run -v /Users/tt/code/mblast/sample:/job ncbi/magicblast magicblast -db /job/sequence.fasta -sra SRR597644 -no_unaligned -splice F -num_threads 8 -out /job/results.sam
Error: (2108.2) [magicblast] VDB 3.0.7: 2024-03-12T18:59:31 . sys: encryption failed while validating token within cryptographic module - Verification issue 0x4008 for this certificate: ( cert. version : 3 serial number : 00 issuer name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification Authority subject name : C=US, O=The Go Daddy Group\, Inc., OU=Go Daddy Class 2 Certification Authority issued on : 2004-06-29 17:06:20 expires on : 2034-06-29 17:06:20 signed using : RSA with SHA1 RSA key size : 2048 bits basic constraints : CA=true )
Error: (2108.2) [magicblast] VDB 3.0.7: 2024-03-12T18:59:31 . sys: mbedtls_ssl_get_verify_result for 'locate.ncbi.nlm.nih.gov' returned 0x4008 ( !! The certificate is not correctly signed by the trusted CA !! The certificate is signed with an unacceptable hash. )
BLAST query/options error: The provided SRA accession 'SRR597644' does not exist
Please refer to the BLAST+ user manual.
I get the same issue when I run "ncbi/magicblast" on an AWS Fargate instance too. Any ideas what could be wrong?
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