Update binaries, ui, cores

Dockerfile

@@ -15,11 +15,12 @@ RUN pip install coverage && \
     pip install pathos
 
 # download StringTie software and untar it
+
 RUN cd /kb/dev_container/modules && \
     mkdir StringTie && cd StringTie && \
-    wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.3b.Linux_x86_64.tar.gz &&\
-    tar xvfz stringtie-1.3.3b.Linux_x86_64.tar.gz && \
-    cd stringtie-1.3.3b.Linux_x86_64 && \
+    wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-2.1.4.Linux_x86_64.tar.gz &&\
+    tar xvfz stringtie-2.1.4.Linux_x86_64.tar.gz && \
+    cd stringtie-2.1.4.Linux_x86_64 && \
     mkdir /kb/deployment/bin/StringTie && \
     cp -R stringtie /kb/deployment/bin/StringTie/stringtie
 
@@ -38,9 +39,9 @@ RUN cd /kb/dev_container/modules && \
 # download gffread script
 RUN cd /kb/dev_container/modules && \
     mkdir gffread && cd gffread && \
-    wget http://ccb.jhu.edu/software/stringtie/dl/gffread-0.9.9.Linux_x86_64.tar.gz &&\
-    tar xvfz gffread-0.9.9.Linux_x86_64.tar.gz && \
-    cd gffread-0.9.9.Linux_x86_64 && \
+    wget http://ccb.jhu.edu/software/stringtie/dl/gffread-0.12.3.Linux_x86_64.tar.gz &&\
+    tar xvfz gffread-0.12.3.Linux_x86_64.tar.gz && \
+    cd gffread-0.12.3.Linux_x86_64 && \
     mkdir /kb/deployment/bin/gffread && \
     cp -R gffread /kb/deployment/bin/gffread/gffread
 
@@ -49,9 +50,9 @@ RUN cd /kb/dev_container/modules && \
 # download gffcompare script
 RUN cd /kb/dev_container/modules && \
     mkdir gffcompare && cd gffcompare && \
-    wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.10.4.Linux_x86_64.tar.gz	 &&\
-    tar xvfz gffcompare-0.10.4.Linux_x86_64.tar.gz	 && \
-    cd gffcompare-0.10.4.Linux_x86_64	 && \
+    wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.12.1.Linux_x86_64.tar.gz	 &&\
+    tar xvfz gffcompare-0.12.1.Linux_x86_64.tar.gz	 && \
+    cd gffcompare-0.12.1.Linux_x86_64	 && \
     mkdir /kb/deployment/bin/gffcompare && \
     cp -R gffcompare /kb/deployment/bin/gffcompare/gffcompare
 

RELEASE_NOTES.md

@@ -38,3 +38,7 @@ Updated citations to PLOS format
 Ran Black
 Reference Chain to clients added
 Updated citations to PLOS format
+
+1.1.6
+* Updated version of binaries
+* Change number of cores passed to each job

kbase.yml

@@ -8,7 +8,7 @@ service-language:
     python
 
 module-version:
-    1.1.5
+    1.1.6
 
 owners:
     [tgu2]

lib/kb_stringtie/Utils/StringTieUtil.py

@@ -817,9 +817,11 @@ def _process_alignment_set_object(self, params):
             alignment_upload_params["alignment_ref"] = alignment_ref
             mul_processor_params.append(alignment_upload_params)
 
-        cpus = max(1, multiprocessing.cpu_count() - 2)
-        pool = Pool(ncpus=cpus)
-        log("running _process_alignment_object with {} cpus".format(cpus))
+        # A max of 20 subtasks for the cbs
+        # A max of two simultaneous
+        worker_pool = 3
+        pool = Pool(ncpus=worker_pool)
+        log("running _process_alignment_object with {} cpus".format(worker_pool))
         alignment_expression_map = pool.map(
             self._process_alignment_object, mul_processor_params
         )

ui/narrative/methods/run_stringtie/display.yaml

@@ -1,7 +1,7 @@
 #
 # Define basic display information
 #
-name     : Assemble Transcripts using StringTie - v1.3.3b
+name     : Assemble Transcripts using StringTie - v2.1.4
 
 tooltip  : |
     Assemble the transcripts from RNA-seq read alignments using StringTie.

ui/narrative/methods/run_stringtie/spec.json

@@ -152,7 +152,7 @@
           "target_property" : "skip_reads_with_no_ref"
         },       
         {
-          "constant_value"  : 2,
+          "constant_value"  : 10,
           "target_property" : "num_threads"
         },      
         {