ncbi / docker Goto Github PK

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ncbi-docker

Container builders for NCBI Utilities

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Docker hub image (ncbi/blast/2.13.0) has signature-related error

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

docker build erroneous with edirect 15.0

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
[...]

✗ 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?

ncbi / docker Goto Github PK

docker's Introduction

ncbi-docker

docker's People

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docker's Issues

Docker hub image (ncbi/blast/2.13.0) has signature-related error

docker build erroneous with edirect 15.0

Update the edirect image

Why does the container have google-cloud-sdk in it?

FATAL: kernel too old

No docker.io/ncbi/blast-static:2.15.0 images

magicblast docker image returning "encryption failed while validating token within cryptographic module"

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