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Makefile
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PIPELINEROOT := ../
include $(PIPELINEROOT)Makefile.common
all: $(VERIFICATIONFILE)
CONVERTER := xlscat
CONVERTEROPT := -s '\t' -S
EXTRACLEANING := perl -i -pe 's/\t +/\t/g; s/ +\t/\t/g; s/ +/ /g'
# Check that all required somewhere are available
global_check:
# clients/interpretors
@which java > [email protected]
@which perl >> [email protected]
@which mysql >> [email protected]
@which R >> [email protected]
@which python3 >> [email protected]
# Ensembl API
@perl -MBio::EnsEMBL::Registry -e 1 >> [email protected]
# other Perl modules
@perl -MArchive::Tar -e 1 >> [email protected]
@perl -MArchive::Zip -e 1 >> [email protected]
@perl -MArray::Utils -e 1 >> [email protected]
@perl -MBio::SeqIO -e 1 >> [email protected]
@perl -MCpanel::JSON::XS -e 1 >> [email protected]
@perl -MData::Dumper -e 1 >> [email protected]
@perl -MDBI -e 1 >> [email protected]
@perl -MDBD::mysql -e 1 >> [email protected]
@perl -MDBD::Pg -e 1 >> [email protected]
@perl -MDigest::SHA -e 1 >> [email protected]
@perl -MExporter -e 1 >> [email protected]
@perl -MFile::Basename -e 1 >> [email protected]
@perl -MFile::Copy -e 1 >> [email protected]
@perl -MFile::Find -e 1 >> [email protected]
@perl -MFile::Path -e 1 >> [email protected]
@perl -MFile::Slurp -e 1 >> [email protected]
@perl -MFile::Spec -e 1 >> [email protected]
@perl -MFindBin -e 1 >> [email protected]
@perl -MGetopt::Long -e 1 >> [email protected]
@perl -MHTTP::Request -e 1 >> [email protected]
@perl -MIO::Compress::Gzip -e 1 >> [email protected]
@perl -MIO::Socket -e 1 >> [email protected]
@perl -MIO::Uncompress::Gunzip -e 1 >> [email protected]
@perl -MLWP::UserAgent -e 1 >> [email protected]
@perl -MLWP::Simple -e 1 >> [email protected]
@perl -MList::Compare -e 1 >> [email protected]
@perl -MList::MoreUtils -e 1 >> [email protected]
@perl -MList::Util -e 1 >> [email protected]
@perl -MParallel::ForkManager -e 1 >> [email protected]
@perl -MSort::Naturally -e 1 >> [email protected]
@perl -MSpreadsheet::Read -e 1 >> [email protected]
@perl -MSpreadsheet::ParseExcel -e 1 >> [email protected]
@perl -MText::CSV -e 1 >> [email protected]
@perl -MSpreadsheet::ParseXLSX -e 1 >> [email protected]
@perl -MSpreadsheet::WriteExcel -e 1 >> [email protected]
@perl -MTest::More -e 1 >> [email protected]
@perl -MTime::HiRes -e 1 >> [email protected]
@perl -MTime::localtime -e 1 >> [email protected]
@perl -MWebservice::InterMine -e 1 >> [email protected]
@perl -MXML::Fast -e 1 >> [email protected]
# R libraries
@R -e 'library("affy")' >> [email protected] 2>/dev/null
@R -e 'library("AnnotationDbi")' >> [email protected] 2>/dev/null
@R -e 'library("BgeeCall")' >> [email protected] 2>/dev/null
@R -e 'library("Biobase")' >> [email protected] 2>/dev/null
@R -e 'library("biomaRt")' >> [email protected] 2>/dev/null
@R -e 'library("Biostrings")' >> [email protected] 2>/dev/null
@R -e 'library("BUSpaRse")' >> [email protected] 2>/dev/null
@R -e 'library("data.table")' >> [email protected] 2>/dev/null
@R -e 'library("dplyr")' >> [email protected] 2>/dev/null
@R -e 'library("DropletUtils")' >> [email protected] 2>/dev/null
@R -e 'library("edgeR")' >> [email protected] 2>/dev/null
@R -e 'library("fdrtool")' >> [email protected] 2>/dev/null
@R -e 'library("forcats")' >> [email protected] 2>/dev/null
@R -e 'library("gcrma")' >> [email protected] 2>/dev/null
@R -e 'library("genefilter")' >> [email protected] 2>/dev/null
@R -e 'library("GenomicFeatures")' >> [email protected] 2>/dev/null
@R -e 'library("ggExtra")' >> [email protected] 2>/dev/null
@R -e 'library("gghighlight")' >> [email protected] 2>/dev/null
@R -e 'library("ggplot2")' >> [email protected] 2>/dev/null
@R -e 'library("gridExtra")' >> [email protected] 2>/dev/null
@R -e 'library("HelpersMG")' >> [email protected] 2>/dev/null
@R -e 'library("LaplacesDemon")' >> [email protected] 2>/dev/null
@R -e 'library("limma")' >> [email protected] 2>/dev/null
@R -e 'library("Matrix")' >> [email protected] 2>/dev/null
@R -e 'library("mclust")' >> [email protected] 2>/dev/null
@R -e 'library("methods")' >> [email protected] 2>/dev/null
@R -e 'library("plyr")' >> [email protected] 2>/dev/null
@R -e 'library("R.utils")' >> [email protected] 2>/dev/null
@R -e 'library("RCurl")' >> [email protected] 2>/dev/null
@R -e 'library("reshape2")' >> [email protected] 2>/dev/null
@R -e 'library("rjson")' >> [email protected] 2>/dev/null
@R -e 'library("Seurat")' >> [email protected] 2>/dev/null
@R -e 'library("stringr")' >> [email protected] 2>/dev/null
@R -e 'library("tools")' >> [email protected] 2>/dev/null
# R annotator script
@R -e 'library("SRAdb")' >> [email protected] 2>/dev/null
@R -e 'library("gsubfn")' >> [email protected] 2>/dev/null
# For topAnat
@R -e 'library("Rgraphviz")' >> [email protected] 2>/dev/null
@R -e 'library("rJava")' >> [email protected] 2>/dev/null
@R -e 'library("Runiversal")' >> [email protected] 2>/dev/null
@R -e 'library("topGO")' >> [email protected] 2>/dev/null
# Extra R libraries required during cel/MAS5 processing
@R -e 'library("celeganscdf")' >> [email protected] 2>/dev/null
@R -e 'library("celegansprobe")' >> [email protected] 2>/dev/null
@R -e 'library("drosgenome1cdf")' >> [email protected] 2>/dev/null
@R -e 'library("drosgenome1probe")' >> [email protected] 2>/dev/null
@R -e 'library("drosophila2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("drosophila2probe")' >> [email protected] 2>/dev/null
@R -e 'library("hgfocuscdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgfocusprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95acdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95bcdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95bprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95ccdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95cprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95dcdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95dprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95ecdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95eprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95av2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu95av2probe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133acdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133a2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133a2probe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133bcdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133bprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133plus2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("hgu133plus2probe")' >> [email protected] 2>/dev/null
@R -e 'library("htmg430acdf")' >> [email protected] 2>/dev/null
@R -e 'library("htmg430aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("hu6800cdf")' >> [email protected] 2>/dev/null
@R -e 'library("hu6800probe")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74acdf")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74av2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74av2probe")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74bv2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74bv2probe")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74cv2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("mgu74cv2probe")' >> [email protected] 2>/dev/null
@R -e 'library("moe430acdf")' >> [email protected] 2>/dev/null
@R -e 'library("moe430aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("moe430bcdf")' >> [email protected] 2>/dev/null
@R -e 'library("moe430bprobe")' >> [email protected] 2>/dev/null
@R -e 'library("mouse4302cdf")' >> [email protected] 2>/dev/null
@R -e 'library("mouse4302probe")' >> [email protected] 2>/dev/null
@R -e 'library("mouse430a2cdf")' >> [email protected] 2>/dev/null
@R -e 'library("mouse430a2probe")' >> [email protected] 2>/dev/null
@R -e 'library("mu11ksubacdf")' >> [email protected] 2>/dev/null
@R -e 'library("mu11ksubaprobe")' >> [email protected] 2>/dev/null
@R -e 'library("mu11ksubbcdf")' >> [email protected] 2>/dev/null
@R -e 'library("mu11ksubbprobe")' >> [email protected] 2>/dev/null
@R -e 'library("rae230acdf")' >> [email protected] 2>/dev/null
@R -e 'library("rae230aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("rgu34acdf")' >> [email protected] 2>/dev/null
@R -e 'library("rgu34aprobe")' >> [email protected] 2>/dev/null
@R -e 'library("rhesuscdf")' >> [email protected] 2>/dev/null
@R -e 'library("rhesusprobe")' >> [email protected] 2>/dev/null
@R -e 'library("zebrafishcdf")' >> [email protected] 2>/dev/null
@R -e 'library("zebrafishprobe")' >> [email protected] 2>/dev/null
# Python libraries for Zebrafish intermine
@python3 -c "import intermine" >> [email protected] 2>/dev/null
@python3 -c "import simplejson" >> [email protected] 2>/dev/null
# Python libraries for download_files/analyze_all_files.ipynb
@python3 -c "import IPython" >> [email protected] 2>/dev/null
@python3 -c "import matplotlib" >> [email protected] 2>/dev/null
@python3 -c "import numpy" >> [email protected] 2>/dev/null
@python3 -c "import os" >> [email protected] 2>/dev/null
@python3 -c "import pandas" >> [email protected] 2>/dev/null
@python3 -c "import seaborn" >> [email protected] 2>/dev/null
# Python libraries for orthologs_paralogs_app
@python3 -c "import SPARQLWrapper" >> [email protected] 2>/dev/null
@python3 -c "import rdflib" >> [email protected] 2>/dev/null
@python3 -c "import isodate" >> [email protected] 2>/dev/null
@python3 -c "import pyparsing" >> [email protected] 2>/dev/null
@python3 -c "import six" >> [email protected] 2>/dev/null
@python3 -c "import configparser" >> [email protected] 2>/dev/null
@python3 -c "import datetime" >> [email protected] 2>/dev/null
@python3 -c "import distutils" >> [email protected] 2>/dev/null
@python3 -c "import multiprocessing" >> [email protected] 2>/dev/null
@python3 -c "import pathlib" >> [email protected] 2>/dev/null
@python3 -c "import typing" >> [email protected] 2>/dev/null
@python3 -c "import ast" >> [email protected] 2>/dev/null
@python3 -c "import errno" >> [email protected] 2>/dev/null
@python3 -c "import fcntl" >> [email protected] 2>/dev/null
@python3 -c "import fileinput" >> [email protected] 2>/dev/null
@python3 -c "import io" >> [email protected] 2>/dev/null
@python3 -c "import json" >> [email protected] 2>/dev/null
@python3 -c "import logging" >> [email protected] 2>/dev/null
@python3 -c "import os" >> [email protected] 2>/dev/null
@python3 -c "import shutil" >> [email protected] 2>/dev/null
@python3 -c "import sys" >> [email protected] 2>/dev/null
@python3 -c "import getopt" >> [email protected] 2>/dev/null
@python3 -c "import time" >> [email protected] 2>/dev/null
## Binaries
# network
@which wget >> [email protected]
@which rsync >> [email protected]
@which git >> [email protected]
# others
@which pipenv >> [email protected]
@which mvn >> [email protected]
@which gunzip >> [email protected]
@which bunzip2 >> [email protected]
@which makeblastdb >> [email protected]
@which blastn >> [email protected]
@which $(CONVERTER) >> [email protected]
# tmpdir with enough free disk space available?
@mkdir -p $(TMPDIR)
@if [[ -d $(TMPDIR) ]]; then echo -n; else echo "Directory [$(TMPDIR)] does not exist" >> [email protected]; exit 6; fi
@if [[ -w $(TMPDIR) ]]; then echo -n; else echo "Directory [$(TMPDIR)] is not writable" >> [email protected]; exit 7; fi
@echo "Think to sync the submodule(s) to get last (develop branch) annotations!"
@$(MV) [email protected] $@
# Build the Bgee Java application needed for some steps
$(PIPELINEROOT)$(BGEEPIPELINEJAR):
@cd $(PIPELINEROOT)$(BGEEAPPDIR)m2_local_repository/; chmod +x mvn-install-file.sh; ./mvn-install-file.sh; $(RM) -r ~/.m2/repository/org/bbop
@cd $(PIPELINEROOT)$(BGEEAPPDIR); mvn clean install --projects bgee-dao-api,bgee-dao-sql,bgee-pipeline; $(CP) bgee-pipeline/target/$(BGEEPIPELINEJARNAME) ../pipeline/pipeline/$(BGEEPIPELINEJAR)
## Install a converter to convert TSV files
#check_converter:
## Check if perl xls converter is there
# @perl -MSpreadsheet::Read -e1 >[email protected]
# @which $(CONVERTER) >> [email protected]
# @$(MV) [email protected] $@
#
#
## Export Affymetrix annotation files
#convert_annotAffy: check_converter $(PIPELINEROOT)$(AFFY_CURATION_FILEPATH)
# # Get xls sheetnames
# @$(CONVERTER) -i $(PIPELINEROOT)$(AFFY_CURATION_FILEPATH) >[email protected] 2>&1
# @echo >>[email protected]
# # Convert affymetrixChip in TSV
# @$(CONVERTER) $(CONVERTEROPT) `grep ' affymetrixChip' [email protected] | sed -e 's/^.* - //; s/: \[.*$$//'` $(PIPELINEROOT)$(AFFY_CURATION_FILEPATH) > $(PIPELINEROOT)$(AFFY_CHIP_FILEPATH)
# @$(EXTRACLEANING) $(PIPELINEROOT)$(AFFY_CHIP_FILEPATH)
# @head -5 $(PIPELINEROOT)$(AFFY_CHIP_FILEPATH) > [email protected]
# @echo >>[email protected]
# # Convert microarrayExperiment in TSV
# @$(CONVERTER) $(CONVERTEROPT) `grep ' microarrayExperiment' [email protected] | sed -e 's/^.* - //; s/: \[.*$$//'` $(PIPELINEROOT)$(AFFY_CURATION_FILEPATH) > $(PIPELINEROOT)$(MICROARRAY_EXPERIMENT_FILEPATH)
# @$(EXTRACLEANING) $(PIPELINEROOT)$(MICROARRAY_EXPERIMENT_FILEPATH)
# @head -5 $(PIPELINEROOT)$(MICROARRAY_EXPERIMENT_FILEPATH) >> [email protected]
# @echo >>[email protected]
# # Convert chipType in TSV
# @$(CONVERTER) $(CONVERTEROPT) `grep ' chipType' [email protected] | sed -e 's/^.* - //; s/: \[.*$$//'` $(PIPELINEROOT)$(AFFY_CURATION_FILEPATH) > $(PIPELINEROOT)$(AFFY_CHIPTYPE_FILEPATH)
# @$(EXTRACLEANING) $(PIPELINEROOT)$(AFFY_CHIPTYPE_FILEPATH)
# @head -5 $(PIPELINEROOT)$(AFFY_CHIPTYPE_FILEPATH) >> [email protected]
# @$(CAT) [email protected] [email protected] > $@
# @$(RM) [email protected] [email protected]
#
## Export RNA_seq annotation files
#convert_annotRNASeq: check_converter $(PIPELINEROOT)$(RNASEQ_CURATION_FILEPATH)
# # Get xls sheetnames
# @$(CONVERTER) -i $(PIPELINEROOT)$(RNASEQ_CURATION_FILEPATH) >[email protected] 2>&1
# @echo >>[email protected]
# # Convert RNAseqExperiment in TSV
# @$(CONVERTER) $(CONVERTEROPT) `grep ' RNAseqExperiment' [email protected] | sed -e 's/^.* - //; s/: \[.*$$//'` $(PIPELINEROOT)$(RNASEQ_CURATION_FILEPATH) > $(PIPELINEROOT)$(RNASEQ_EXPERIMENT_FILEPATH)
# @$(EXTRACLEANING) $(PIPELINEROOT)$(RNASEQ_EXPERIMENT_FILEPATH)
# @head -5 $(PIPELINEROOT)$(RNASEQ_EXPERIMENT_FILEPATH) > [email protected]
# @echo >>[email protected]
# # Convert RNAseqLibrary in TSV
# @$(CONVERTER) $(CONVERTEROPT) `grep ' RNAseqLibrary' [email protected] | sed -e 's/^.* - //; s/: \[.*$$//'` $(PIPELINEROOT)$(RNASEQ_CURATION_FILEPATH) > $(PIPELINEROOT)$(RNASEQ_LIB_FILEPATH)
# @$(EXTRACLEANING) $(PIPELINEROOT)$(RNASEQ_LIB_FILEPATH)
# @head -5 $(PIPELINEROOT)$(RNASEQ_LIB_FILEPATH) >> [email protected]
# @$(CAT) [email protected] [email protected] > $@
# @$(RM) [email protected] [email protected]
#FIXME used?
# Export homology annotation file
$(PIPELINEROOT)$(SIMILARITYFILEPATH): $(CONVERTER) $(PIPELINEROOT)$(SIMILARITY_CURATION_FILEPATH)
@$(CONVERTER) $(CONVERTEROPT) 01 $(PIPELINEROOT)$(SIMILARITY_CURATION_FILEPATH) > $@
@$(EXTRACLEANING) $@
build_container:
@which apptainer
apptainer build ${PIPELINE_CONTAINER_FILE} ${PIPELINE_CONTAINER_NAME}.def 2>&1 > [email protected]
@$(MV) [email protected] $@
test_container: build_container
# clients/interpretors
@$(PIPELINE_CONTAINER_CMD) which java > [email protected]
@$(PIPELINE_CONTAINER_CMD) which perl >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which mysql >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which R >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which python3 >> [email protected]
# Ensembl API
@$(PIPELINE_CONTAINER_CMD) perl -MBio::EnsEMBL::Registry -e 1 >> [email protected]
# other Perl modules
@$(PIPELINE_CONTAINER_CMD) perl -MArchive::Tar -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MArchive::Zip -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MArray::Utils -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MBio::SeqIO -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MCpanel::JSON::XS -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MData::Dumper -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MDBI -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MDBD::mysql -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MDBD::Pg -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MDigest::SHA -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MExporter -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFile::Basename -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFile::Copy -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFile::Find -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFile::Path -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFile::Slurp -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFile::Spec -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MFindBin -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MGetopt::Long -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MHTTP::Request -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MIO::Compress::Gzip -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MIO::Socket -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MIO::Uncompress::Gunzip -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MLWP::Simple -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MLWP::UserAgent -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MList::Compare -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MList::MoreUtils -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MList::Util -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MParallel::ForkManager -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MSort::Naturally -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MSpreadsheet::Read -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MSpreadsheet::ParseExcel -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MText::CSV -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MSpreadsheet::ParseXLSX -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MSpreadsheet::WriteExcel -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MTest::More -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MTime::HiRes -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MTime::localtime -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MWebservice::InterMine -e 1 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) perl -MXML::Fast -e 1 >> [email protected]
# R libraries
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("affy")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("AnnotationDbi")' >> [email protected] 2>/dev/null
#@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("BgeeCall")' >> [email protected] 2>/dev/null #FIXME issue with the source tarball build at Bioconductor
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("Biobase")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("biomaRt")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("Biostrings")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("BUSpaRse")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("data.table")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("dplyr")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("DropletUtils")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("edgeR")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("fdrtool")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("forcats")' >> [email protected] 2>/dev/null #FIXME not loaded as usual, will maybe not be used!
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("gcrma")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("genefilter")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("GenomicFeatures")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("ggExtra")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("gghighlight")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("ggplot2")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("gridExtra")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("HelpersMG")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("LaplacesDemon")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("limma")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("Matrix")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mclust")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("methods")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("plyr")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("R.utils")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("RCurl")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("reshape2")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rjson")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("Seurat")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("stringr")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("tools")' >> [email protected] 2>/dev/null
# R annotator script
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("SRAdb")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("gsubfn")' >> [email protected] 2>/dev/null
# For topAnat
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("Rgraphviz")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rJava")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("Runiversal")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("topGO")' >> [email protected] 2>/dev/null
# Extra R libraries required during cel/MAS5 processing
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("celeganscdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("celegansprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("drosgenome1cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("drosgenome1probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("drosophila2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("drosophila2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgfocuscdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgfocusprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95bcdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95bprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95ccdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95cprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95dcdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95dprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95ecdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95eprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95av2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu95av2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133a2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133a2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133bcdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133bprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133plus2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hgu133plus2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("htmg430acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("htmg430aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hu6800cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("hu6800probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74av2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74av2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74bv2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74bv2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74cv2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mgu74cv2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("moe430acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("moe430aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("moe430bcdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("moe430bprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mouse4302cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mouse4302probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mouse430a2cdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mouse430a2probe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mu11ksubacdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mu11ksubaprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mu11ksubbcdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("mu11ksubbprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rae230acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rae230aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rgu34acdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rgu34aprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rhesuscdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("rhesusprobe")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("zebrafishcdf")' >> [email protected] 2>/dev/null
@$(PIPELINE_CONTAINER_CMD) R -q -e 'library("zebrafishprobe")' >> [email protected] 2>/dev/null
# Python libraries for Zebrafish intermine
@$(PIPELINE_CONTAINER_CMD) python3 -c "import intermine" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import simplejson" >> [email protected]
# Python libraries for download_files/analyze_all_files.ipynb
@$(PIPELINE_CONTAINER_CMD) python3 -c "import IPython" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import matplotlib" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import numpy" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import os" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import pandas" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import seaborn" >> [email protected]
# Python libraries for Sagane's annotation scripts
# TODO ...
# Python libraries for Sagane's H5AD scripts
# TODO ...
# Python libraries for orthologs_paralogs_app
@$(PIPELINE_CONTAINER_CMD) python3 -c "import SPARQLWrapper" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import rdflib" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import isodate" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import pyparsing" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import six" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import configparser" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import datetime" >> [email protected]
#@$(PIPELINE_CONTAINER_CMD) python3 -c "import distutils" >> [email protected] #FIXME no more in Python 3.12+ ?
@$(PIPELINE_CONTAINER_CMD) python3 -c "import multiprocessing" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import pathlib" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import typing" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import ast" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import errno" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import fcntl" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import fileinput" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import io" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import json" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import logging" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import os" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import shutil" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import sys" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import getopt" >> [email protected]
@$(PIPELINE_CONTAINER_CMD) python3 -c "import time" >> [email protected]
# others
@$(PIPELINE_CONTAINER_CMD) which pipenv >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which mvn >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which gunzip >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which bunzip2 >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which makeblastdb >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which blastn >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which kallisto >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which bustools >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which fastp >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which fasterq-dump >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which gtf_to_fasta >> [email protected]
@$(PIPELINE_CONTAINER_CMD) which $(CONVERTER) >> [email protected]
@$(MV) [email protected] $@
$(VERIFICATIONFILE): global_check $(PIPELINEROOT)$(SIMILARITYFILEPATH) $(PIPELINEROOT)$(BGEEPIPELINEJAR) convert_annotAffy convert_annotRNASeq
# create empty file or clean existing file
@touch [email protected]
# verifications for homology annotation file
@echo ---------- $(SIMILARITYFILE)--------- >> [email protected]
@{ echo "Line count: \c" && wc -l < $(PIPELINEROOT)$(SIMILARITYFILEPATH); } >> [email protected]
@echo 5 first lines: >> [email protected]
@head -5 $(PIPELINEROOT)$(SIMILARITYFILEPATH) >> [email protected]
# verifications for Affymetrix annotation file
@echo ---------- AFFYMETRIX ANNOTATIONS --------- >> [email protected]
@{ echo "Line count in microarray experiments: \c" && wc -l < $(PIPELINEROOT)$(MICROARRAY_EXPERIMENT_FILEPATH); } >> [email protected]
@{ echo "Line count in affymetrix chips: \c" && wc -l < $(PIPELINEROOT)$(AFFY_CHIP_FILEPATH); } >> [email protected]
@{ echo "Line count in affymetrix chip types: \c" && wc -l < $(PIPELINEROOT)$(AFFY_CHIPTYPE_FILEPATH); } >> [email protected]
@echo 5 first lines of each file: >> [email protected]
@$(CAT) convert_annotAffy >> [email protected]
@$(MV) [email protected] $@
clean:
-@$(RM) global_check $(CONVERTER) $(PIPELINEROOT)$(SIMILARITYFILEPATH) $(PIPELINEROOT)$(BGEEPIPELINEJAR) $(VERIFICATIONFILE) convert_annotAffy convert_annotRNASeq check_converter *.tmp *.temp