finalizes v0.1.8

Author: nellore

eval/preprocess_all_of_GEUVADIS.sh

@@ -7,4 +7,4 @@ RAILHOME=~/rail
 # Set output directory here -- must be on S3!
 OUTPUT=s3://rail-eu-west-1/geuvprepped
 
-python $RAILHOME/src prep elastic -m GEUVADIS_all_descriptive_staged.manifest -c 2 --core-instance-bid-price 0.35 --master-instance-bid-price 0.35 --core-instance-type c3.2xlarge --master-instance-type c3.2xlarge -o $OUTPUT --no-consistent-view -f --region eu-west-1 --do-not-check-manifest
+python $RAILHOME/src prep elastic -m GEUVADIS_all_descriptive_staged.manifest -c 1 -o $OUTPUT -f --region eu-west-1 --do-not-check-manifest --ec2-key-name raileuw1

eval/run_single_sample_sim.sh

@@ -128,7 +128,7 @@ echo 'Computing precision and recall...'
 (cat Aligned.out.sam | $PYTHON $RAILHOME/eval/mapping_accuracy.py -t $DATADIR/${SAMPLE}_sim.bed -c 0.1 >${PERFORMANCE}_mapping_accuracy_SC_summary) &
 wait
 # Move Subjunc results to final destination
-mv $OUTPUT/subjunc $MAINOUTPUT
+mv $OUTPUT/subjunc $SAMPLEOUTPUT
 echo 'Running HISAT on sample '${SAMPLE}' with no annotation and in paired-end mode...'
 echo '#'${SAMPLE}' HISAT 1-pass noann paired' >>$TIMELOG
 mkdir -p $OUTPUT/hisat/noann_paired_1pass

releases/install_rail-rna-0.1.8

@@ -923,7 +923,7 @@ def run(self, mode, payload):
                 ec2_key_name=args.ec2_key_name,
                 keep_alive=args.keep_alive,
                 termination_protected=args.termination_protected,
-                no_consistent_view=args.no_consistent_view,
+                consistent_view=args.consistent_view,
                 no_direct_copy=args.no_direct_copy,
                 check_manifest=(not args.do_not_check_manifest),
                 intermediate_lifetime=args.intermediate_lifetime,
@@ -989,7 +989,7 @@ def run(self, mode, payload):
                 ec2_key_name=args.ec2_key_name,
                 keep_alive=args.keep_alive,
                 termination_protected=args.termination_protected,
-                no_consistent_view=args.no_consistent_view,
+                consistent_view=args.consistent_view,
                 no_direct_copy=args.no_direct_copy,
                 intermediate_lifetime=args.intermediate_lifetime,
                 max_task_attempts=args.max_task_attempts
@@ -1025,7 +1025,7 @@ def run(self, mode, payload):
                 ec2_key_name=args.ec2_key_name,
                 keep_alive=args.keep_alive,
                 termination_protected=args.termination_protected,
-                no_consistent_view=args.no_consistent_view,
+                consistent_view=args.consistent_view,
                 no_direct_copy=args.no_direct_copy,
                 check_manifest=(not args.do_not_check_manifest),
                 intermediate_lifetime=args.intermediate_lifetime,

releases/install_rail-rna-devel

@@ -228,13 +228,15 @@ def run_job_flow(branding, json_config, force, no_browser=False,
             if 'bad request' in str(e).lower():
                 raise RuntimeError('(' + str(e) + ');'
                                 + (' ensure that IAM roles are '
-                                'configured properly, and try again. This '
+                                'configured properly. This '
                                 'may require talking to your AWS account '
                                 'admin. See '
                                 'http://docs.aws.amazon.com/ElasticMapReduce/'
                                 'latest/DeveloperGuide/emr-'
                                 'iam-roles-defaultroles.html for more '
-                                'information.'))
+                                'information. In most cases, the solution '
+                                'to is to run "aws emr '
+                                'create-default-roles", and try again.'))
             else:
                 raise
         json_response = json.load(job_flow_response)

releases/install_rail-rna-v0.1.8

@@ -363,10 +363,12 @@ def presorted_tasks(input_files, process_id, sort_options, output_dir,
                                                     % process_id
                                                 )):
                 sort_command = (('set -eo pipefail; gzip -cd %s | '
-                                 '%s -S %d %s | '
+                                 '%s -S %d %s -t$\'%s\' | '
                                  'gzip -c -%d >%s')
                                     % (sort,
-                                        unsorted_file, memcap, sort_options,
+                                        unsorted_file, memcap,
+                                        sort_options,
+                                        separator.encode('string_escape'),
                                         gzip_level,
                                         unsorted_file[:-12] + '.gz'))
                 try:
@@ -389,8 +391,11 @@ def presorted_tasks(input_files, process_id, sort_options, output_dir,
                                                     '*.%s.unsorted'
                                                     % process_id
                                                 )):
-                sort_command = '%s -S %d %s %s >%s' % (sort, memcap,
+                sort_command = '%s -S %d %s -t$\'%s\' %s >%s' % (sort, memcap,
                                                             sort_options,
+                                                            separator.encode(
+                                                                'string_escape'
+                                                            ),
                                                             unsorted_file,
                                                             unsorted_file[:-9])
                 try:
@@ -523,14 +528,18 @@ def step_runner_with_error_return(streaming_command, input_glob, output_dir,
             # Reducer. Merge sort the input glob.
             if gzip:
                 # Use process substitution
-                prefix = '(%s -S %d %s -m %s' % (sort, memcap, sort_options,
+                prefix = '(%s -S %d %s -t$\'%s\' -m %s' % (
+                        sort, memcap, sort_options,
+                        separator.encode('string_escape'),
                         ' '.join(['<(gzip -cd %s)' % input_file
                                     for input_file in input_files]) + ')'
                     )
             else:
                 # Reducer. Merge sort the input glob.
-                prefix = '%s -S %d %s -m %s' % (sort, memcap, sort_options,
-                                                    input_glob)
+                prefix = '%s -S %d %s -t$\'%s\' -m %s' % (sort, memcap,
+                                            sort_options,
+                                            separator.encode('string_escape'),
+                                            input_glob)
         err_file = os.path.abspath(os.path.join(err_dir, (
                                             ('%d.log' % task_id)
                                                 if attempt_number is None

releases/install_rail-rna-vdevel

@@ -1 +1 @@
-∀ Rail-RNA v0.1.7d
+∀ Rail-RNA vdevel