Make database downloadble on macOS

notebooks/AlphaFold.ipynb

@@ -167,7 +167,7 @@
         "      %shell mkdir -p /opt/conda/lib/python3.7/site-packages/alphafold/common/\n",
         "      %shell cp -f /content/stereo_chemical_props.txt /opt/conda/lib/python3.7/site-packages/alphafold/common/\n",
         "\n",
-        "      %shell mkdir --parents \"{PARAMS_DIR}\"\n",
+        "      %shell mkdir -p \"{PARAMS_DIR}\"\n",
         "      %shell wget -O \"{PARAMS_PATH}\" \"{SOURCE_URL}\"\n",
         "      pbar.update(27)\n",
         "\n",

scripts/download_alphafold_params.sh

@@ -34,8 +34,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/params"
 SOURCE_URL="https://storage.googleapis.com/alphafold/alphafold_params_2022-03-02.tar"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
   --directory="${ROOT_DIR}" --preserve-permissions
 rm "${ROOT_DIR}/${BASENAME}"

scripts/download_bfd.sh

@@ -36,8 +36,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/bfd"
 SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt.tar.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
   --directory="${ROOT_DIR}"
 rm "${ROOT_DIR}/${BASENAME}"

scripts/download_mgnify.sh

@@ -36,8 +36,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/mgnify"
 SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/mgy_clusters_2018_12.fa.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${BASENAME}"
 popd

scripts/download_pdb70.sh

@@ -34,8 +34,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/pdb70"
 SOURCE_URL="http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/old-releases/pdb70_from_mmcif_200401.tar.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
   --directory="${ROOT_DIR}"
 rm "${ROOT_DIR}/${BASENAME}"

scripts/download_pdb_mmcif.sh

@@ -44,7 +44,7 @@ echo "If the download speed is too slow, try changing the mirror to:"
 echo "  * rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ (Europe)"
 echo "  * ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ (Asia)"
 echo "or see https://www.wwpdb.org/ftp/pdb-ftp-sites for more download options."
-mkdir --parents "${RAW_DIR}"
+mkdir -p "${RAW_DIR}"
 rsync --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 \
   rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ \
   "${RAW_DIR}"
@@ -53,7 +53,7 @@ echo "Unzipping all mmCIF files..."
 find "${RAW_DIR}/" -type f -iname "*.gz" -exec gunzip {} +
 
 echo "Flattening all mmCIF files..."
-mkdir --parents "${MMCIF_DIR}"
+mkdir -p "${MMCIF_DIR}"
 find "${RAW_DIR}" -type d -empty -delete  # Delete empty directories.
 for subdir in "${RAW_DIR}"/*; do
   mv "${subdir}/"*.cif "${MMCIF_DIR}"
@@ -62,4 +62,4 @@ done
 # Delete empty download directory structure.
 find "${RAW_DIR}" -type d -empty -delete
 
-aria2c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"
+aria2c -c "ftp://ftp.wwpdb.org/pub/pdb/data/status/obsolete.dat" --dir="${ROOT_DIR}"

scripts/download_pdb_seqres.sh

@@ -34,5 +34,5 @@ ROOT_DIR="${DOWNLOAD_DIR}/pdb_seqres"
 SOURCE_URL="ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"

scripts/download_small_bfd.sh

@@ -34,8 +34,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/small_bfd"
 SOURCE_URL="https://storage.googleapis.com/alphafold-databases/reduced_dbs/bfd-first_non_consensus_sequences.fasta.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${BASENAME}"
 popd

scripts/download_uniclust30.sh

@@ -36,8 +36,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/uniclust30"
 SOURCE_URL="https://storage.googleapis.com/alphafold-databases/casp14_versions/uniclust30_2018_08_hhsuite.tar.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 tar --extract --verbose --file="${ROOT_DIR}/${BASENAME}" \
   --directory="${ROOT_DIR}"
 rm "${ROOT_DIR}/${BASENAME}"

scripts/download_uniprot.sh

@@ -41,9 +41,9 @@ SPROT_SOURCE_URL="ftp://ftp.ebi.ac.uk/pub/databases/uniprot/current_release/know
 SPROT_BASENAME=$(basename "${SPROT_SOURCE_URL}")
 SPROT_UNZIPPED_BASENAME="${SPROT_BASENAME%.gz}"
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
-aria2c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${TREMBL_SOURCE_URL}" --dir="${ROOT_DIR}"
+aria2c -c "${SPROT_SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${TREMBL_BASENAME}"
 gunzip "${ROOT_DIR}/${SPROT_BASENAME}"

scripts/download_uniref90.sh

@@ -34,8 +34,8 @@ ROOT_DIR="${DOWNLOAD_DIR}/uniref90"
 SOURCE_URL="ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz"
 BASENAME=$(basename "${SOURCE_URL}")
 
-mkdir --parents "${ROOT_DIR}"
-aria2c "${SOURCE_URL}" --dir="${ROOT_DIR}"
+mkdir -p "${ROOT_DIR}"
+aria2c -c "${SOURCE_URL}" --dir="${ROOT_DIR}"
 pushd "${ROOT_DIR}"
 gunzip "${ROOT_DIR}/${BASENAME}"
 popd