database

[NK181092]

I am following the steps to download PADLOC, the first two steps are working. As soon as I reach padloc--db-update, it is giving error that no such files is present

check the path, and indeed the database file is missing

[leightonpayne]

Hi @NK181092,

Can you please post the exact code you are trying to run, and the resulting error message?

[NK181092]

Following the steps as mentionned to install the package. As soon as it comes to update database, I am getting this error.

Unpacking database... tar (child): /home/jp/miniconda3/envs/padloc/data/data.tar.gz: Cannot open: No such file or directory tar (child): Error is not recoverable: exiting now tar: Child returned status 2 tar: Error is not recoverable: exiting now

I tried to install the database manually by putting it in the above mentionned path and when I am testing the software, it is giving me error of not being able to access the hmm files.

[leightonpayne]

I have a feeling this may be an issue with your curl installation? The tar error suggests that the compressed database has not been downloaded correctly.

Could you please try to run the following, and post the output:

DBREPO="https://github.com/padlocbio/padloc-db"
DATA="/home/jp/miniconda3/envs/padloc/data/"
VERSION="v2.0.0"

# Download compressed PADLOC data
echo ">> Running curl"
curl --version
curl -sL "${DBREPO}/archive/refs/tags/${VERSION}.tar.gz" --output ${DATA}/data.tar.gz
test -f "${DATA}/data.tar.gz" && echo ">> curl WORKED" || echo ">> curl FAILED"

# Uncompress PADLOC data
echo ">> Running tar"
tar --version
tar -xzf ${DATA}/data.tar.gz --directory ${DATA} --strip-components 1 && rm ${DATA}/data.tar.gz

[NK181092]

Thank You, Issue resolved