add env variable propagation via -e flag

impy.py

@@ -39,12 +39,13 @@ CONTAINER_CODE_DIR = '/home/imp/code'
 @click.option('-b', '--binning-method', help="Binning method to use.",  type=click.Choice(['maxbin', 'no']), default='maxbin')
 @click.option('-c', '--config-file-path', help='Set different config file path.')
 @click.option('-d', '--database-path', help='Set different database path.', default=IMP_DEFAULT_DB_DIR)
+@click.option('-e', '--environment', help='Add an environment variable (-e <key>=<value>).', multiple=True)
 @click.option('-s', '--source-code', help='Use IMP source code at the file path specified instead of the one shipped inside the image.')
 @click.option('--threads', default=4, help='Number of threads to use')
 @click.option('--memtotal', default=8, help='Cap of memory to use for megahit in GB.')
 @click.option('--memcore', default=2, help='Memory allowed per core for samtools in GB.')
 @click.pass_context
-def cli(ctx, image_name, image_tag, image_repo, threads, memtotal, assembler, binning_method, memcore, database_path, config_file_path, source_code, enter):
+def cli(ctx, image_name, image_tag, image_repo, threads, memtotal, assembler, binning_method, memcore, database_path, config_file_path, source_code, enter, environment):
     """Integrated Metaomic Pipeline"""
     if not ctx.obj:
         ctx.obj = {}
@@ -93,6 +94,10 @@ def cli(ctx, image_name, image_tag, image_repo, threads, memtotal, assembler, bi
         click.secho("`database path` must be a directory.", fg='red', bold=True)
         ctx.abort()
 
+    ctx.obj['environment'] = {}
+    for value in environment:
+        k, v = value.split('=')
+        ctx.obj['environment'][k] = v
     # # TODO # add environment variables
     # envs = ['-e {}="{}"'.format(*e.split('=')) for e in args['-e']]
 
@@ -378,7 +383,7 @@ def init(ctx, generate, index):
         ctx.abort()
     click.secho('IMP image found', fg='green')
 
-    ev = {}
+    ev = ctx.obj['environment']
 
     # check if fasta file is provided
     if index:
@@ -522,17 +527,15 @@ def preprocessing(ctx, metagenomic, metranscriptomic,
         click.secho('Metatranscriptomic data should be 2 paired files.', fg='red', bold=True)
         ctx.abort()
 
-
-    ev = {
-        'IMP_BINNING_METHOD': ctx.obj['binning-method'],
-        'MEMTOTAL': ctx.obj['memtotal'],
-        'MEMCORE': ctx.obj['memcore'],
-        'THREADS': ctx.obj['threads'],
-        'MG': ' '.join(mg_data),
-        'MT': ' '.join(mt_data),
-        'IMP_ASSEMBLER': ctx.obj['assembler'],
-        'IMP_STEPS': ' '.join(steps)
-    }
+    ev =  ctx.obj['environment']
+    ev['IMP_BINNING_METHOD'] = ctx.obj['binning-method']
+    ev['MEMTOTAL'] = ctx.obj['memtotal']
+    ev['MEMCORE'] = ctx.obj['memcore']
+    ev['THREADS'] = ctx.obj['threads']
+    ev['MG'] = ' '.join(mg_data)
+    ev['MT'] = ' '.join(mt_data)
+    ev['IMP_ASSEMBLER'] = ctx.obj['assembler']
+    ev['IMP_STEPS'] = ' '.join(steps)
     if no_filtering:
         ev['PREPROCESSING_FILTERING'] = False
     if screen:
@@ -672,15 +675,14 @@ def assembly(ctx, metagenomic, metranscriptomic,
         ctx.abort()
 
     # <-- end assembly validation
+    ev =  ctx.obj['environment']
+    ev['IMP_BINNING_METHOD'] = ctx.obj['binning-method']
+    ev['MEMTOTAL'] = ctx.obj['memtotal']
+    ev['MEMCORE'] = ctx.obj['memcore']
+    ev['THREADS'] = ctx.obj['threads']
+    ev['IMP_ASSEMBLER'] = ctx.obj['assembler']
+    ev['IMP_STEPS'] = ' '.join(steps)
 
-    ev = {
-        'IMP_BINNING_METHOD': ctx.obj['binning-method'],
-        'MEMTOTAL': ctx.obj['memtotal'],
-        'MEMCORE': ctx.obj['memcore'],
-        'THREADS': ctx.obj['threads'],
-        'IMP_ASSEMBLER': ctx.obj['assembler'],
-        'IMP_STEPS': ' '.join(steps)
-    }
     if mg_data:
         ev['MG'] = ' '.join(mg_data)
     if mt_data:
@@ -812,14 +814,12 @@ def analysis(ctx, data_dir, single_omics,
               and assembly_dir.files('mt.reads.sorted.bam')):
         click.secho("`Assembly directory` must contains mg and mt data. e.g: mgmt.assembly.merged.fa, mg.reads.sorted.bam, mg.reads.sorted.bam", fg='red', bold=True)
         ctx.abort()
-
-    ev = {
-        'IMP_BINNING_METHOD': ctx.obj['binning-method'],
-        'MEMTOTAL': ctx.obj['memtotal'],
-        'MEMCORE': ctx.obj['memcore'],
-        'THREADS': ctx.obj['threads'],
-        'IMP_STEPS': ' '.join(steps)
-    }
+    ev =  ctx.obj['environment']
+    ev['IMP_BINNING_METHOD'] = ctx.obj['binning-method']
+    ev['MEMTOTAL'] = ctx.obj['memtotal']
+    ev['MEMCORE'] = ctx.obj['memcore']
+    ev['THREADS'] = ctx.obj['threads']
+    ev['IMP_STEPS'] = ' '.join(steps)
     if mg_data:
         ev['MG'] = ' '.join(mg_data)
     if mt_data:
@@ -922,13 +922,12 @@ def binning(ctx, data_dir, single_omics,
     if single_omics:
         mt_data = []
 
-    ev = {
-        'IMP_BINNING_METHOD': ctx.obj['binning-method'],
-        'MEMTOTAL': ctx.obj['memtotal'],
-        'MEMCORE': ctx.obj['memcore'],
-        'THREADS': ctx.obj['threads'],
-        'IMP_STEPS': ' '.join(steps)
-    }
+    ev =  ctx.obj['environment']
+    ev['IMP_BINNING_METHOD'] = ctx.obj['binning-method']
+    ev['MEMTOTAL'] = ctx.obj['memtotal']
+    ev['MEMCORE'] = ctx.obj['memcore']
+    ev['THREADS'] = ctx.obj['threads']
+    ev['IMP_STEPS'] = ' '.join(steps)
     if mg_data:
         ev['MG'] = ' '.join(mg_data)
     if mt_data: