Bash repeating my directory and can not call the file-CodePudding

have to use a .sh script to unpack and prep some databases. The code is the following:

#
# Downloads and unzips all required data for AlphaFold.
#
# Usage: bash download_all_data.sh /path/to/download/directory
set -e

DOWNLOAD_DIR="$1"

for f in $(ls ${DOWNLOAD_DIR}/*.tar.gz)
do
  tar --extract --verbose --file="${DOWNLOAD_DIR}/${f}" /
      --directory="${DOWNLOAD_DIR}/mmseqs_dbs"
  rm "${f}"
  BASENAME="$(basename {f%%.*})"
  DB_NAME="${BASENAME}_db"
  OLD_PWD=$(pwd)
  cd "${DOWNLOAD_DIR}/mmseqs_dbs" 
  mmseqs tar2exprofiledb "${BASENAME}" "${DB_NAME}"
  mmseqs createindex "${DB_NAME}" "${DOWNLOAD_DIR}/tmp/"
  cd "${OLD_PWD}"
done

When I run the code, I got that error:

(openfold_venv) watson@watson:~/pedro/openfold$ sudo bash scripts/prep_mmseqs_dbs.sh data/
tar: data//data//colabfold_envdb_202108.tar.gz: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now

I don`t understand why the code repeats my "DOWNLOAD_DIR", the correct should be :

data/colabfold_envdb_202108.tar.gz

and not

data//data//colabfold_envdb_202108.tar.gz

Could anyone help me?

New code:

set -e

DOWNLOAD_DIR="$1"

for f in ${DOWNLOAD_DIR}/*.tar.gz; 
do
  tar --extract --verbose --file="$f" /
      --directory="${DOWNLOAD_DIR}/mmseqs_dbs"
  rm "${f}"
  BASENAME="$(basename {f%%.*})"
  DB_NAME="${BASENAME}_db"
  OLD_PWD=$(pwd)
  cd "${DOWNLOAD_DIR}/mmseqs_dbs" 
  mmseqs tar2exprofiledb "${BASENAME}" "${DB_NAME}"
  mmseqs createindex "${DB_NAME}" "${DOWNLOAD_DIR}/tmp/"
  cd "${OLD_PWD}"
done

CodePudding user response：

To answer your first question: why is it repeating? Because you are repeating it in your code:

for f in ${DOWNLOAD_DIR}/*.tar.gz; 
do
  tar --extract --verbose --file="${DOWNLOAD_DIR}/$f"

If f is downloads/file.tar.gz then ${DOWNLOAD_DIR}/${f} will resolve to downloads/downloads/file.tar.tgz.

As to your second question: the escape character is the backslash \, not the forward slash. Your multiline command should look like this:

tar --extract --verbose --file="${DOWNLOAD_DIR}/${f}" \
    --directory="${DOWNLOAD_DIR}/mmseqs_dbs"