fix toil on OSX

EOSC-LOFAR · Jan 14, 2018 · db6f9bb · db6f9bb
1 parent eebef21
commit db6f9bb
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Showing 4 changed files with 4 additions and 2 deletions.
diff --git a/Makefile b/Makefile
@@ -53,7 +53,7 @@ run-udocker: .virtualenv/bin/udocker steps/ndppp_prep_cal.cwl .virtualenv/bin/cw
 		prefactor.cwl \
 		jobs/job_20sb.yaml > >(tee $(RUN)/output) 2> >(tee $(RUN)/log >&2)
 
-run: data/$(SMALL)/ .virtualenv/bin/cwltool steps/ndppp_prep_cal.cwl
+run: .virtualenv/bin/cwltool steps/ndppp_prep_cal.cwl
 	mkdir -p $(RUN)
 	.virtualenv/bin/cwltool \
 		--leave-tmpdir \
@@ -67,6 +67,8 @@ toil: data/$(SMALL)/ .virtualenv/bin/cwltoil steps/ndppp_prep_cal.cwl
 	.virtualenv/bin/toil-cwl-runner \
 		--logFile $(RUN)/log \
 		--outdir $(RUN)/results \
+		--tmp-outdir-prefix $(PWD)/tmp \
+		--workDir $(PWD)/work \
 		--jobStore file://$(RUN)/job_store \
 		prefactor.cwl \
 		jobs/job_20sb.yaml | tee $(RUN)/output

diff --git a/requirements.txt b/requirements.txt
@@ -1,6 +1,6 @@
 #cwlref-runner
 html5lib
--e git://github.com/BD2KGenomics/toil.git@7f23f6d7905c35a5e6238b97a7825c13a7e174c8#egg=toil[cwl,mesos,google]
+-e git://github.com/BD2KGenomics/toil.git@682aa3a8b36aab9d187b0b08ef3509a62973ac85#egg=toil[cwl,mesos,google]
 boto
 pycrypto
 protobuf

diff --git a/tmp/.phony b/tmp/.phony
diff --git a/work/.phony b/work/.phony