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Fixes for Slingshot Dockerfile and other various minor bugs #25

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Fixes for Slingshot Dockerfile and other various minor bugs #25

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12a7d45
docker key change
yutuyt01 May 24, 2024
5ca4716
os.sep change for cross-os
yutuyt01 May 28, 2024
45a0ae5
patchwork fix for slingshot dockerfile and changed clusters=1 to be c…
yutuyt01 May 30, 2024
f95b9d1
included pyyaml in requirements as it was not present previously
yutuyt01 Jun 11, 2024
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2 changes: 1 addition & 1 deletion BoolODE/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -264,7 +264,7 @@ def do_post_processing(self):
for gsampPath in generatedPaths[jobid]:
settings = {}
invalid = False
settings['outPrefix'] = gsampPath + '/' + gsampPath.split('/')[-1] + '-ss'
settings['outPrefix'] = gsampPath + '/' + gsampPath.split(os.sep)[-1] + '-ss'
settings['expr'] = Path(gsampPath\
,'ExpressionData.csv')
settings['pseudo'] = Path(gsampPath\
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1 change: 1 addition & 0 deletions requirements.txt
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Expand Up @@ -5,3 +5,4 @@ tqdm==4.31.1
seaborn==0.9.0
pandas==0.24.2
scikit-learn==0.21.3
pyyaml==6.0.1
11 changes: 7 additions & 4 deletions scripts/runSlingshot.py
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Expand Up @@ -23,7 +23,7 @@
def parseArgs(args):
parser = OptionParser()

parser.add_option('', '--outPrefix', type = 'str',default='',
parser.add_option('', '--outPrefix', type = 'str', default='',
help='Prefix for output files.')

parser.add_option('-e', '--expr', type='str',
Expand Down Expand Up @@ -70,8 +70,10 @@ def computeSSPT(ExpDF, ptDF, nClust, outPaths, noEnd = False, perplexity = 500):
'''
if nClust == 1:
# Return simulation time as PseduoTime
for outPath in outPaths:
ptDF.loc[ExpDF.columns].to_csv(outPath+"/PseudoTime.csv", columns =['Time'])
ptDF.loc[ExpDF.columns].to_csv(outPaths + "/PseudoTime.csv", columns=['Time'])
# for outPath in outPaths:
# print(outPath)
# ptDF.loc[ExpDF.columns].to_csv(outPath+"/PseudoTime.csv", columns =['Time'])

else:
### Compute PseudoTime ordering using slingshot
Expand Down Expand Up @@ -212,7 +214,8 @@ def computeSSPT(ExpDF, ptDF, nClust, outPaths, noEnd = False, perplexity = 500):
tn.to_csv(outPaths+"/Updated_rd.tsv",
sep='\t')
plt.savefig(outPaths+"/SlingshotOutput.png")
os.system("rm -rf temp/")
if sys.platform.startswith("linux"):
os.system("rm -rf temp/")

def main(args):
opts, args = parseArgs(args)
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10 changes: 5 additions & 5 deletions slingshot-docker/Dockerfile
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Expand Up @@ -35,11 +35,11 @@ RUN apt-get install -y libssl-dev libcurl4-openssl-dev libgsl-dev\
##############
## Install R
RUN echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial-cran35/" | tee -a /etc/apt/sources.list && \
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 && \
gpg -a --export E084DAB9 | apt-key add - && \
apt-get update && \
apt-get install -y r-recommended=${R_VERSION} && \
apt-get install -y r-base=${R_VERSION}
gpg --keyserver keyserver.ubuntu.com --recv-key 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7 && \
gpg -a --export 95C0FAF38DB3CCAD0C080A7BDC78B2DDEABC47B7 | apt-key add - && \
apt-get update --allow-unauthenticated && \
apt-get install -y --allow-unauthenticated r-recommended=${R_VERSION} && \
apt-get install -y --allow-unauthenticated r-base=${R_VERSION}
RUN Rscript -e 'install.packages("BiocManager", repos = "http://cran.us.r-project.org")'

##############
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