Pick curl or wget based on availability

Snakefile

@@ -56,14 +56,22 @@ rule wrangle_metadata:
         wrangle_metadata_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/scripts/wrangle_metadata.py",
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
-        cd bin
-        [[ -f wrangle_metadata.py ]] || wget {params.wrangle_metadata_url}
-        chmod 755 *
-        cd ..
+
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/wrangle_metadata.py ]] || $download_cmd bin/wrangle_metadata.py {params.wrangle_metadata_url}
+        chmod +x bin/*
         
+        # (3) Run the script
         python3 ./bin/wrangle_metadata.py --metadata {input.metadata} \
             --strain-id {params.strain_id} \
             --output {output.metadata}
@@ -264,14 +272,22 @@ rule final_strain_name:
         set_final_strain_name_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/scripts/set_final_strain_name.py",
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
+         # (1) Pick curl or wget based on availability
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
-        cd bin
-        [[ -f set_final_strain_name.py ]] || wget {params.set_final_strain_name_url}
-        chmod 755 *
-        cd ..
 
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/set_final_strain_name.py ]] || $download_cmd bin/set_final_strain_name.py {params.set_final_strain_name_url}
+        chmod +x bin/*
+        
+        # (3) Run the script
         python3 bin/set_final_strain_name.py \
             --metadata {input.metadata} \
             --input-auspice-json {input.auspice_json} \

ingest/workflow/snakemake_rules/fetch_sequences.smk

@@ -23,15 +23,24 @@ rule fetch_from_genbank:
         genbank_url_url="https://raw.githubusercontent.com/nextstrain/dengue/ca659008bfbe4b3f799e11ecd106a0b95977fe93/ingest/bin/genbank-url", # Update if dengue merged
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
-        cd bin
-        [[ -f csv-to-ndjson ]] || wget {params.csv_to_ndjson_url}
-        [[ -f genbank-url ]] || wget {params.genbank_url_url}
-        [[ -f fetch-from-genbank ]] || wget {params.fetch_from_genbank_url}
-        chmod 755 *
-        cd ..
+
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/csv-to-ndjson ]]      || $download_cmd bin/csv-to-ndjson {params.csv_to_ndjson_url}
+        [[ -f bin/genbank-url ]]        || $download_cmd bin/genbank-url {params.genbank_url_url}
+        [[ -f bin/fetch-from-genbank ]] || $download_cmd bin/fetch-from-genbank {params.fetch_from_genbank_url}
+        chmod +x bin/*
+
+        # (3) Fetch the sequences
         ./bin/fetch-from-genbank {params.serotype_tax_id} > {output.genbank_ndjson}
         """
 

ingest/workflow/snakemake_rules/slack_notifications.smk

@@ -31,16 +31,22 @@ rule notify_on_genbank_record_change:
         notify_on_record_change_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/notify-on-record-change",
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
-        fi
-        if [[ ! -f bin/notify-on-record-change ]]; then
-          cd bin
-          wget {params.notify_on_record_change_url}
-          chmod 755
-          cd ..
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
 
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/notify-on-record-change ]] || $download_cmd bin/notify-on-record-change {params.notify_on_record_change_url}
+        chmod +x bin/*
+
+        # (3) Run the script
         ./bin/notify-on-record-change {input.genbank_ndjson} {params.s3_src:q}/genbank.ndjson.xz Genbank
         """
 
@@ -55,15 +61,22 @@ rule notify_on_metadata_diff:
         notify_on_diff_url = "https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/notify-on-diff",
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
-        fi
-        if [[ ! -f bin/notify-on-diff ]]; then
-          cd bin
-          wget {params.notify_on_diff_url}
-          chmod 755
-          cd ..
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
+
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/notify-on-diff ]] || $download_cmd bin/notify-on-diff {params.notify_on_diff_url}
+        chmod +x bin/*
+
+        # (3) Run the script
         ./bin/notify-on-diff {input.metadata} {params.s3_src:q}/metadata.tsv.gz
         """
 

ingest/workflow/snakemake_rules/transform.smk

@@ -20,7 +20,18 @@ rule fetch_general_geolocation_rules:
         geolocation_rules_url=config["transform"]["geolocation_rules_url"],
     shell:
         """
-        curl {params.geolocation_rules_url} > {output.general_geolocation_rules}
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
+        fi
+
+        # (2) Fetch general geolocation rules
+        $download_cmd {output.general_geolocation_rules} {params.geolocation_rules_url}
         """
 
 
@@ -73,22 +84,30 @@ rule transform:
         ndjson_to_tsv_and_fasta_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/ndjson-to-tsv-and-fasta",
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
-        cd bin
-        [[ -f transform-field-names ]]      || wget {params.transform_field_names_url}
-        [[ -f transform-string-fields ]]    || wget {params.transform_string_fields_url}
-        [[ -f transform-strain-names ]]     || wget {params.transform_strain_names_url}
-        [[ -f transform-date-fields ]]      || wget {params.transform_date_fields_url}
-        [[ -f transform-genbank-location ]] || wget {params.transform_genbank_location_url}
-        [[ -f transform-authors ]]          || wget {params.transform_authors_url}
-        [[ -f apply-geolocation-rules ]]    || wget {params.apply_geolocation_rules_url}
-        [[ -f merge-user-metadata ]]        || wget {params.merge_user_metadata_url}
-        [[ -f ndjson-to-tsv-and-fasta ]]    || wget {params.ndjson_to_tsv_and_fasta_url}
-        chmod 755 *
-        cd ..
 
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/transform-field-names ]]      || $download_cmd bin/transform-field-names {params.transform_field_names_url}
+        [[ -f bin/transform-string-fields ]]    || $download_cmd bin/transform-string-fields {params.transform_string_fields_url}
+        [[ -f bin/transform-strain-names ]]     || $download_cmd bin/transform-strain-names {params.transform_strain_names_url}
+        [[ -f bin/transform-date-fields ]]      || $download_cmd bin/transform-date-fields {params.transform_date_fields_url}
+        [[ -f bin/transform-genbank-location ]] || $download_cmd bin/transform-genbank-location {params.transform_genbank_location_url}
+        [[ -f bin/transform-authors ]]          || $download_cmd bin/transform-authors {params.transform_authors_url}
+        [[ -f bin/apply-geolocation-rules ]]    || $download_cmd bin/apply-geolocation-rules {params.apply_geolocation_rules_url}
+        [[ -f bin/merge-user-metadata ]]        || $download_cmd bin/merge-user-metadata {params.merge_user_metadata_url}
+        [[ -f bin/ndjson-to-tsv-and-fasta ]]    || $download_cmd bin/ndjson-to-tsv-and-fasta {params.ndjson_to_tsv_and_fasta_url}
+        chmod +x bin/*
+
+        # (3) Transform the sequences
         (cat {input.sequences_ndjson} \
             | ./bin/transform-field-names \
                 --field-map {params.field_map} \
@@ -131,14 +150,22 @@ rule post_process_metadata:
 
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
-        cd bin
-        [[ -f post_process_metadata.py ]] || wget {params.post_process_metadata_url}
-        chmod 755 *
-        cd ..
 
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/post_process_metadata.py ]] || $download_cmd bin/post_process_metadata.py {params.post_process_metadata_url}
+        chmod +x bin/*
+
+        # (3) Post-process the metadata
         ./bin/post_process_metadata.py --metadata {input.metadata} --outfile {output.metadata}
         """
 

ingest/workflow/snakemake_rules/trigger_rebuild.smk

@@ -17,14 +17,21 @@ rule trigger_build:
         trigger_on_new_data_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/trigger-on-new-data"
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
-        fi
-        if [[ ! -f bin/trigger-on-new-data ]]; then
-          cd bin
-          wget {params.trigger_on_new_data_url}
-          chmod 755 *
-          cd ..
+        # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
+
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/trigger-on-new-data ]] || $download_cmd bin/trigger-on-new-data {params.trigger_on_new_data_url}
+        chmod +x bin/*
+
+        # (3) Trigger the build
         ./bin/trigger-on-new-data {input.metadata_upload} {input.fasta_upload}
         """

ingest/workflow/snakemake_rules/upload.smk

@@ -59,15 +59,24 @@ rule upload_to_s3:
         cloudfront_invalidate_url="https://raw.githubusercontent.com/nextstrain/monkeypox/644d07ebe3fa5ded64d27d0964064fb722797c5d/ingest/bin/cloudfront-invalidate"
     shell:
         """
-        if [[ ! -d bin ]]; then
-          mkdir bin
+         # (1) Pick curl or wget based on availability    
+        if which curl > /dev/null; then
+            download_cmd="curl -fsSL --output"
+        elif which wget > /dev/null; then
+            download_cmd="wget -O"
+        else
+            echo "ERROR: Neither curl nor wget found. Please install one of them."
+            exit 1
         fi
-        cd bin
-        [[ -f upload-to-s3 ]] || wget {params.upload_to_s3_url}
-        [[ -f sha256sum ]] || wget {params.sha256sum_url}
-        [[ -f cloudfront-invalidate ]] || wget {params.cloudfront_invalidate_url}
-        chmod 755 *
-        cd ..
+
+        # (2) Download the required scripts if not already present
+        [[ -d bin ]] || mkdir bin
+        [[ -f bin/upload-to-s3 ]]          || $download_cmd bin/upload-to-s3 {params.upload_to_s3_url}
+        [[ -f bin/sha256sum ]]             || $download_cmd bin/sha256sum {params.sha256sum_url}
+        [[ -f bin/cloudfront-invalidate ]] || $download_cmd bin/cloudfront-invalidate {params.cloudfront_invalidate_url}
+        chmod +x bin/*
+
+        # (3) Run the upload script
         ./bin/upload-to-s3 \
             {params.quiet} \
             {input.file_to_upload:q} \