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egaffo / CirComPara

:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
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TypeError: cannot concatenate 'str' and 'int' objects: #9

Closed pecoraro90 closed 1 year ago

pecoraro90 commented 1 year ago

Hi, I am using the docker and I am having the following error:

(base) user@NGS:~/CirComPara$ sudo docker run --rm -it -v $(pwd):/ data egaffo/circompara-docker scons: Reading SConscript files ... 'adapter' not defined for file./data/LNCAP-AD-rep1_1.fastq, sample S1. Sk ipping. 'adapter' not defined for file./data/LNCAP-AD-rep1_2.fastq, sample S1. Sk ipping. 'adapter' not defined for file./data/LNCAP-AD-rep2_1.fastq, sample S2. Sk ipping. 'adapter' not defined for file./data/LNCAP-AD-rep2_2.fastq, sample S2. Sk ipping. 'adapter' not defined for file./data/LNCAP-AI-rep1_1.fastq, sample S3. Sk ipping. 'adapter' not defined for file./data/LNCAP-AI-rep1_2.fastq, sample S3. Sk ipping. 'adapter' not defined for file./data/LNCAP-AI-rep2_1.fastq, sample S4. Sk ipping. 'adapter' not defined for file./data/LNCAP-AI-rep2_2.fastq, sample S4. Sk ipping. TypeError: cannot concatenate 'str' and 'int' objects: File "/CirComPara/src/ccp_main.scons", line 356: exports = '''env_check_indexes''') File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 604: return method(*args, kw) File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 541: return _SConscript(self.fs, *files, *subst_kw) File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 250: exec file in call_stack[-1].globals File "/CirComPara/src/ccp_check_indexes.scons", line 117: exports = '''env_build_indexes ''') File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 604: return method(args, kw) File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 541: return _SConscript(self.fs, *files, subst_kw) File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 250: exec file in call_stack[-1].globals File "/CirComPara/src/ccp_build_indexes.scons", line 67: exports = '''env_index_hisat2 ''') File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 604: return method(*args, *kw) File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 541: return _SConscript(self.fs, files, subst_kw) File "/CirComPara/tools/scons/scons-local-2.5.1/SCons/Script/SConscript .py", line 250: exec file in call_stack[-1].globals File "/CirComPara/src/ccp_index_hisat2.scons", line 44: ''' ${TARGETS[0].dir}''' + os.path.sep + target_basename + ''' ''' + EXTRA_PARAMS

Do you have any suggestion to fix it?

thanks

egaffo commented 1 year ago

This repository is no more maintained. Please, use the newer CirComPara2. Check also the CirComPara2 article here.