Merge branch 'dev' into ISS-185

rhysnewell · Jan 11, 2024 · a729b01 · a729b01
2 parents e999d55 + 5eb3ed4
commit a729b01
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diff --git a/README.md b/README.md
@@ -57,7 +57,12 @@ conda env create -n aviary -f aviary.yml
 conda activate aviary
 pip install -e .
 ```
+The `aviary` executable can then be run from any directory. Since the code in
+this directory is then used for running, any updates made there will be
+immediately available. We recommend this mode for developing and debugging
+aviary.
 
+## Checking installation
 Whatever option you choose, running `aviary --help` should return the following
 output:
 
@@ -86,22 +91,6 @@ Utility modules:
 
 ```
 
-Upon first running aviary you will be prompted to input the location for where you would like
-your conda environments to be stored, the GTDB release installed on your system, the location of your
-EnrichM database, and the location of your BUSCO database. These locations will be stored as environment
-variables, but for aviary to be able to use those environment variables you will have to either source your .bashrc
-or reactivate your conda environment depending on whether you installed aviary within a conda environment or not:
-
-```
-conda deactivate; conda activate aviary
-
-OR
-
-source ~/.bashrc
-```
-
-These environment variables can be reset using `aviary configure`
-
 ## Databases
 
 Aviary uses programs which require access to locally stored databases. 
@@ -111,7 +100,7 @@ The **required** databases are as follows:
 * [GTDB](https://gtdb.ecogenomic.org/downloads)
 * [EggNog](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#setup)
 * [CheckM2](https://github.com/chklovski/CheckM2)
-
+* [SingleM](https://wwood.github.io/singlem/)
 
 ### Installing databases
 

diff --git a/aviary/aviary.py b/aviary/aviary.py
@@ -100,6 +100,17 @@ def str2bool(v):
     else:
         raise argparse.ArgumentTypeError('Boolean value expected.')
 
+def add_workflow_arg(parser, default, help=None):
+    if help is None:
+        help = 'Main workflow to run. This is the snakemake target rule to run.'
+    parser.add_argument(
+        '-w', '--workflow',
+        help=help,
+        dest='workflow',
+        nargs="+",
+        default=default,
+    )
+
 def main():
     if len(sys.argv) == 1 or sys.argv[1] == '-h' or sys.argv[1] == '--help':
         phelp()
@@ -875,13 +886,7 @@ def main():
 
 
 
-    assemble_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['complete_assembly_with_qc'],
-    )
+    add_workflow_arg(assemble_options, ['complete_assembly_with_qc'])
 
     ##########################  ~ RECOVER ~   ###########################
 
@@ -905,13 +910,7 @@ def main():
         required=False,
     )
 
-    recover_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['recover_mags'],
-    )
+    add_workflow_arg(recover_options, ['recover_mags'])
 
     recover_options.add_argument(
         '--perform-strain-analysis', '--perform_strain_analysis',
@@ -945,13 +944,7 @@ def main():
         required=False,
     )
 
-    annotate_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['annotate'],
-    )
+    add_workflow_arg(annotate_options, ['annotate'])
 
     ##########################  ~ diversity ~   ###########################
 
@@ -976,13 +969,7 @@ def main():
         required=False,
     )
 
-    diversity_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['lorikeet'],
-    )
+    add_workflow_arg(diversity_options, ['lorikeet'])
 
     diversity_options.add_argument(
         '--perform-strain-analysis', '--perform_strain_analysis',
@@ -1018,13 +1005,7 @@ def main():
         required=True,
     )
 
-    cluster_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['complete_cluster'],
-    )
+    add_workflow_arg(cluster_options, ['complete_cluster'])
 
     ##########################  ~ VIRAL ~   ###########################
 
@@ -1040,13 +1021,7 @@ def main():
  
                                           ''')
 
-    viral_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['create_webpage_genotype'],
-    )
+    add_workflow_arg(viral_options, ['create_webpage_genotype'])
 
     ##########################   ~ COMPLETE ~  ###########################
 
@@ -1071,13 +1046,7 @@ def main():
         required=False,
     )
 
-    complete_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run',
-        dest='workflow',
-        nargs="+",
-        default=['get_bam_indices', 'recover_mags', 'annotate', 'lorikeet'],
-    )
+    add_workflow_arg(complete_options, ['get_bam_indices', 'recover_mags', 'annotate', 'lorikeet'])
 
     ##########################  ~ ISOLATE ~  ###########################
 
@@ -1093,13 +1062,7 @@ def main():
                                  
                                              ''')
 
-    isolate_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflows to run',
-        dest='workflow',
-        nargs="+",
-        default=['circlator'],
-    )
+    add_workflow_arg(isolate_options, ['circlator'])
 
     ##########################   ~ BATCH ~  ###########################
 
@@ -1174,12 +1137,10 @@ def main():
         default='95'
     )
 
-    batch_options.add_argument(
-        '-w', '--workflow',
-        help='Main workflow to run for each sample',
-        dest='workflow',
-        nargs="+",
-        default=['get_bam_indices', 'recover_mags', 'annotate', 'lorikeet'],
+    add_workflow_arg(
+        batch_options,
+        ['get_bam_indices', 'recover_mags', 'annotate', 'lorikeet'],
+        help='Main workflow (snakemake target rule) to run for each sample'
     )
 
     ##########################   ~ configure ~  ###########################
@@ -1231,13 +1192,7 @@ def main():
         required=False,
     )
 
-    configure_options.add_argument(
-        '-w', '--workflow',
-        help=argparse.SUPPRESS,
-        dest='workflow',
-        nargs="+",
-        default=['download_databases'],
-    )
+    add_workflow_arg(configure_options, ['download_databases'], help=argparse.SUPPRESS)
 
     ###########################################################################
     # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
@@ -1346,6 +1301,8 @@ def manage_env_vars(args):
             args.eggnog_db_path = Config.get_software_db_path('EGGNOG_DATA_DIR', '--eggnog-db-path')
         if args.checkm2_db_path is None:
             args.checkm2_db_path = Config.get_software_db_path('CHECKM2DB', '--checkm2-db-path')
+        if args.singlem_metapackage_path is None:
+            args.singlem_db_path = Config.get_software_db_path('SINGLEM_METAPACKAGE_PATH', '--singlem-metapackage-path')
     except AttributeError:
         pass
 

diff --git a/aviary/modules/Snakefile b/aviary/modules/Snakefile
@@ -2,9 +2,11 @@
 # ruleorder: filtlong_no_reference > link_reads
 
 onsuccess:
+    shell("chmod g+w {log}")
     print("Aviary finished, no error")
 
 onerror:
+    shell("chmod g+w {log}")
     print("An error occurred")
 
 onstart:
@@ -44,6 +46,7 @@ onstart:
 from snakemake.utils import min_version
 import os
 min_version("6.0")
+os.umask(0o002)
 
 module qc:
     snakefile: "quality_control/qc.smk"

diff --git a/aviary/modules/binning/binning.smk b/aviary/modules/binning/binning.smk
@@ -629,32 +629,15 @@ rule das_tool:
         mem_mb = lambda wildcards, attempt: min(int(config["max_memory"])*1024, 512*1024*attempt),
         runtime = lambda wildcards, attempt: 12*60*attempt,
     output:
-        das_tool_done = "data/das_tool_bins_pre_refine/done"
+        touch("data/das_tool_bins_pre_refine/done")
     conda:
         "envs/das_tool.yaml"
     log:
         "logs/das_tool.log"
     benchmark:
         "benchmarks/das_tool.benchmark.txt"
-    shell:
-        """
-        Fasta_to_Scaffolds2Bin.sh -i data/metabat_bins_sspec -e fa > data/metabat_bins_sspec.tsv 2> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/metabat_bins_ssens -e fa > data/metabat_bins_ssens.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/metabat_bins_sens -e fa > data/metabat_bins_sens.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/metabat_bins_spec -e fa > data/metabat_bins_spec.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/concoct_bins -e fa > data/concoct_bins.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/maxbin2_bins -e fasta > data/maxbin_bins.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/vamb_bins/bins -e fna > data/vamb_bins.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/rosella_refined/final_bins/ -e fna > data/rosella_refined_bins.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/metabat2_refined/final_bins/ -e fna > data/metabat2_refined_bins.tsv 2>> {log}; 
-        Fasta_to_Scaffolds2Bin.sh -i data/semibin_refined/final_bins/ -e fna > data/semibin_refined_bins.tsv 2>> {log}; 
-        scaffold2bin_files=$(find data/*bins*.tsv -not -empty -exec ls {{}} \; | tr "\n" ',' | sed "s/,$//g"); 
-        DAS_Tool --search_engine diamond --write_bin_evals 1 --write_bins 1 -t {threads} --score_threshold -42 \
-         -i $scaffold2bin_files \
-         -c {input.fasta} \
-         -o data/das_tool_bins_pre_refine/das_tool >> {log} 2>&1 && \
-        touch data/das_tool_bins_pre_refine/done
-        """
+    script:
+        "scripts/das_tool.py"
 
 rule refine_dastool:
     input:

diff --git a/aviary/modules/binning/envs/das_tool.yaml b/aviary/modules/binning/envs/das_tool.yaml
@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - das_tool = 1.1.2
+  - extern = 0.4.1
diff --git a/aviary/modules/binning/scripts/das_tool.py b/aviary/modules/binning/scripts/das_tool.py
@@ -0,0 +1,58 @@
+import logging
+import os
+import sys
+
+import extern
+
+if __name__ == '__main__':
+    unrefined_binners_to_use = [
+        ('concoct', 'fa'),
+        ('maxbin2', 'fasta'),
+        ('vamb', 'fna')]
+    refined_binners_to_use = [
+        ('rosella', 'fna'),
+        ('semibin', 'fna')]
+
+    # N.B. specifying "metabat" will skip both MetaBAT1 and MetaBAT2.
+    metabats = ['metabat_sspec', 'metabat_ssens', 'metabat_sens', 'metabat_spec']
+
+    binners = []
+    for (binner, extension) in unrefined_binners_to_use:
+        if binner not in snakemake.config['skip_binners']:
+            binners.append((f'{binner}_bins/', extension, f'data/{binner}_bins.tsv'))
+
+    for (binner, extension) in refined_binners_to_use:
+        if binner not in snakemake.config['skip_binners']:
+            binners.append((binner+'_refined/final_bins/', extension, f'data/{binner}_refined_bins.tsv'))
+
+    for metabat in metabats:
+        if metabat not in snakemake.config['skip_binners']:
+            binners.append((metabat.replace('metabat','metabat_bins'), 'fa', f'data/{metabat}_bins.tsv'))
+    if 'metabat2' not in snakemake.config['skip_binners']:
+        binners.append(('metabat2_refined/final_bins/', 'fna', f'data/metabat2_refined_bins.tsv'))
+
+    logfile = snakemake.log[0]
+    logging.basicConfig(filename=logfile, level=logging.INFO)
+    logging.info("Using the following binners: " + str(binners))
+
+    if len(binners) == 0:
+        logging.error("All binners have been skipped, so DAS_tool cannot be run.")
+        sys.exit(1)
+
+    bin_definition_files = []
+    for binner, extension, bin_definition_file in binners:
+        extern.run(f'Fasta_to_Scaffolds2Bin.sh -i data/{binner} -e {extension} >{bin_definition_file}  2>> {logfile}')
+        if os.path.getsize(bin_definition_file) == 0:
+            logging.warning(f'Bin definition file {bin_definition_file} is empty, suggesting that {binner} failed or did not not create any output bins.')
+        else:
+            bin_definition_files.append(bin_definition_file)
+    logging.info("Bin definition files created: " + str(bin_definition_files))
+
+    scaffold2bin_files = ','.join(bin_definition_files)
+
+    das_tool_command = f'DAS_Tool --search_engine diamond --write_bin_evals 1 --write_bins 1 -t {snakemake.threads} --score_threshold -42 \
+        -i {scaffold2bin_files} \
+        -c {snakemake.input.fasta} \
+        -o data/das_tool_bins_pre_refine/das_tool >> {logfile} 2>&1'
+    logging.info("Running DAS_Tool with command: " + das_tool_command)
+    extern.run(das_tool_command)