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Makefile.example
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Makefile.example
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BASE_DIR = ${HOME}/.local
BASE_BIN_DIR = ${BASE_DIR}/bin
# All scripts will be installed in this subdir
# and linked from the parent. This will allow
# for the uninstallation of everything!
APPS_SUBDIR = ccls_sequencing
# There is a difference between 34 and 35. I don't know exactly what it is
# but 35 finds nothing and 34 finds a bunch. Perhaps a change in parameters?
# 34 also requires a few tweeks just to get it to compile? (34 is 5 years older than 35)
#BLAT = blatSrc34
# for some reason 2.2.25+ seems to be installed?
#BLAST = ncbi-blast-2.2.27+-src/c++
#BOWTIE = bowtie-0.12.8
# There are newer versions of bowtie2 out, but seg faults at runtime
# I just installed that latest binaries which do not.
# bowtie2-2.1.0
BOWTIE2 = bowtie2-2.0.0-beta7
# There is an even newer version of trinity
#TRINITY = trinityrnaseq_r2012-06-08
#TRINITY = trinityrnaseq_r2012-10-05
BWA = bwa-0.6.2
PRICE = PriceSource120527
RAY = Ray-20121031
VELVET = Velvet-20121031
# mkdir will raise error if dir exists
# mkdir -p will not and would create full path
MKDIR = mkdir -p
# In the preferred compilation order ...
#
# could eventually add Vicuna and Mira
#
#
# As this is outdated and we don't (not allowed to) install these
# anymore, removing them from list to avoid accidents.
#
#TARGETS = blat bowtie bowtie2 blast bwa trinity price velvet ray
#TARGETS = bowtie2 bwa price velvet ray
TARGETS =
# the @ prefix means the line will be executed, but not printed
# Do I need the &&s? Why not just multiple lines?
# The &&s are a condition so if the first part fails, the next will NOT run.
# Each line is its own thing so if a cd is used, needs to be same line.
# all is the default target that is used when none are given
#all: blat bowtie bowtie2 blast bwa trinity price
#all: bowtie2 bwa price
all: make-all $(TARGETS)
@printf "\nDONE MAKING ALL\n\n"
make-all:
@printf "\nMAKING ALL\n\n"
#install: all
#install: install_all install_bowtie install_bowtie2 install_blat install_blast install_trinity install_bwa install_price install_scripts
#install: install_all install_bowtie install_bowtie2 install_blat install_bwa install_price install_scripts
install: install-all $(TARGETS:%=install-%) install-scripts
@printf "\nDONE INSTALLING ALL\n\n"
@printf "Add $(BASE_BIN_DIR) TO YOUR PATH\n\n"
install-all:
@printf "\nINSTALLING ALL\n\n"
$(MKDIR) $(BASE_BIN_DIR)/$(APPS_SUBDIR)
ultra-clean-scripts:
@printf "\nARCHIVING ALL PREVIOUSLY INSTALLED CCLS SCRIPTS\n\n"
$(MKDIR) $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts
# moving to a subdir rather than deleting, just in case
# sadly, move fails if source file doesn't exist
# Appending the line with "; true" makes make ignore the error.
mv $(BASE_BIN_DIR)/1000genomes_group_multiple_samples.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/1000genomes_group_results.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/add_descriptions_to_results.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/align_herv_k113_chimerics_to_index.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/archive.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_1000genomes.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_bam_to_herv_k113_overlappers.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_exec_on_all.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_fastq_to_herv_k113_overlappers.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_remove_1000genomes_pid_files.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_sqs_demo.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_start_1000genomes_node.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/aws_start_1000genomes_processing.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_extract_sequences_from_fasta.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_extract_uniq_sequences_from_fasta.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_fasta_extractor.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_fastq_2_fasta.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_file_format_detector.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_lane_fasta.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_lane_fastq.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_random_fasta_generator.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_select_random_sequences_from_fasta.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bioruby_split_fasta_file.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blast_check.gawk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blast_check.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_check.gawk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_check.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_cleanup.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_cleanup.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_nt.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_to_sqlite_db.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blastn_wrapper.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blatoutcandidate.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/blatoutcandidate.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/bowtie_human_genomic.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/candidate_non_human.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/candidate_non_human.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/check_sequence_names.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/chopreads.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/clean_fasta_file.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/compress.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/dark.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/dark_OLD.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/ec_blastn_merge.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/ec_fasta_split_and_blast.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/ec_fasta_split_and_blastn.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/ec_fasta_split_and_bowtie.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/ec_quick_dark.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/fasta_read_length_filter.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/fasta_read_split.awk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/fasta_read_split.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/fasta_size_split.awk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/fasta_size_split.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/fastq2fasta.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/file_format_detector.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/herv_adjacent_comparison.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/herv_k113_integration.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/herv_trim_comparison.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/human_genomic_fasta_to_bowtie_index.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/insertion_points_to_table.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/just_first_contig_match_results.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/lines_not_in_reference_list.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/modify_trinity_output.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/overlapper_insertion_points_to_fasta.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/overlapper_seeker.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/overlappers_reference_to_table.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/overlappers_to_table.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/pieces_check.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/pieces_merge.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/positions_within_10bp.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/positions_within_10bp_of_reference.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/pull_reads_fasta.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/pull_reads_fasta.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/quick_dark.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/remove_N_reads_from_fasta.awk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/remove_N_reads_from_fasta.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/remove_human_with_bowtie2.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/rins.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/rins.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/rins_ccls_lib.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/sam2names.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/sam2names.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/sam_to_bam.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/samtools_bam_to_fasta.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/samtools_bam_to_paired_fastq.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/samtools_depth_comparison.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/samtools_extract_aligned_reads.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/samtools_extract_and_clip_chimeric_reads.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/samtools_extract_half_mapped_pairs.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/select_no_hits_from_blast.awk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/select_no_hits_from_blast.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/sequencing_lib.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/simple_queue.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/simple_queue_cron.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/simple_queue_eval.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/simple_queue_pop_to_script.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/spacify_sequence_names.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_bam2fastx_fastq.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_blast.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_blastn_to_nt.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_bowtie2.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_ec_quick_dark.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_fastq_to_fasta.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_fastx_collapser.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_gunzip.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_herv_k113_integration.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_lane_fastq.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_overlapper_seeker.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_bam2fq.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_bam_to_paired_fastq.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_depth_comparison.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_extract_aligned_reads.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_extract_and_clip_chimeric_reads.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_extract_half_mapped_pairs.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_sam_to_bam.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_samtools_sort_bam_by_name.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/srun_trinity.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/to_table.gawk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/trim_alignments_and_descriptions.awk $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/trim_alignments_and_descriptions.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/underscore_sequence_names.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/uniquify_sequence_names.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/write_result.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
mv $(BASE_BIN_DIR)/write_result.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)_make_ultra-clean-scripts/; true
# rm -f $(BASE_BIN_DIR)/1000genomes_group_multiple_samples.sh
# rm -f $(BASE_BIN_DIR)/1000genomes_group_results.sh
# rm -f $(BASE_BIN_DIR)/add_descriptions_to_results.rb
# rm -f $(BASE_BIN_DIR)/align_herv_k113_chimerics_to_index.sh
# rm -f $(BASE_BIN_DIR)/archive.sh
# rm -f $(BASE_BIN_DIR)/aws_1000genomes.sh
# rm -f $(BASE_BIN_DIR)/aws_bam_to_herv_k113_overlappers.sh
# rm -f $(BASE_BIN_DIR)/aws_exec_on_all.sh
# rm -f $(BASE_BIN_DIR)/aws_fastq_to_herv_k113_overlappers.sh
# rm -f $(BASE_BIN_DIR)/aws_remove_1000genomes_pid_files.sh
# rm -f $(BASE_BIN_DIR)/aws_sqs_demo.sh
# rm -f $(BASE_BIN_DIR)/aws_start_1000genomes_node.sh
# rm -f $(BASE_BIN_DIR)/aws_start_1000genomes_processing.sh
# rm -f $(BASE_BIN_DIR)/bioruby_extract_sequences_from_fasta.rb
# rm -f $(BASE_BIN_DIR)/bioruby_extract_uniq_sequences_from_fasta.rb
# rm -f $(BASE_BIN_DIR)/bioruby_fasta_extractor.rb
# rm -f $(BASE_BIN_DIR)/bioruby_fastq_2_fasta.rb
# rm -f $(BASE_BIN_DIR)/bioruby_file_format_detector.rb
# rm -f $(BASE_BIN_DIR)/bioruby_lane_fasta.rb
# rm -f $(BASE_BIN_DIR)/bioruby_lane_fastq.rb
# rm -f $(BASE_BIN_DIR)/bioruby_random_fasta_generator.rb
# rm -f $(BASE_BIN_DIR)/bioruby_select_random_sequences_from_fasta.rb
# rm -f $(BASE_BIN_DIR)/bioruby_split_fasta_file.rb
# rm -f $(BASE_BIN_DIR)/blast_check.gawk
# rm -f $(BASE_BIN_DIR)/blast_check.sh
# rm -f $(BASE_BIN_DIR)/blastn_check.gawk
# rm -f $(BASE_BIN_DIR)/blastn_check.sh
# rm -f $(BASE_BIN_DIR)/blastn_cleanup.pl
# rm -f $(BASE_BIN_DIR)/blastn_cleanup.rb
# rm -f $(BASE_BIN_DIR)/blastn_nt.sh
# rm -f $(BASE_BIN_DIR)/blastn_to_sqlite_db.sh
# rm -f $(BASE_BIN_DIR)/blastn_wrapper.sh
# rm -f $(BASE_BIN_DIR)/blatoutcandidate.pl
# rm -f $(BASE_BIN_DIR)/blatoutcandidate.rb
# rm -f $(BASE_BIN_DIR)/bowtie_human_genomic.sh
# rm -f $(BASE_BIN_DIR)/candidate_non_human.pl
# rm -f $(BASE_BIN_DIR)/candidate_non_human.rb
# rm -f $(BASE_BIN_DIR)/check_sequence_names.rb
# rm -f $(BASE_BIN_DIR)/chopreads.pl
# rm -f $(BASE_BIN_DIR)/clean_fasta_file.rb
# rm -f $(BASE_BIN_DIR)/compress.pl
# rm -f $(BASE_BIN_DIR)/dark.rb
# rm -f $(BASE_BIN_DIR)/dark_OLD.rb
# rm -f $(BASE_BIN_DIR)/ec_blastn_merge.sh
# rm -f $(BASE_BIN_DIR)/ec_fasta_split_and_blast.sh
# rm -f $(BASE_BIN_DIR)/ec_fasta_split_and_blastn.sh
# rm -f $(BASE_BIN_DIR)/ec_fasta_split_and_bowtie.sh
# rm -f $(BASE_BIN_DIR)/ec_quick_dark.sh
# rm -f $(BASE_BIN_DIR)/fasta_read_length_filter.sh
# rm -f $(BASE_BIN_DIR)/fasta_read_split.awk
# rm -f $(BASE_BIN_DIR)/fasta_read_split.sh
# rm -f $(BASE_BIN_DIR)/fasta_size_split.awk
# rm -f $(BASE_BIN_DIR)/fasta_size_split.sh
# rm -f $(BASE_BIN_DIR)/fastq2fasta.pl
# rm -f $(BASE_BIN_DIR)/file_format_detector.rb
# rm -f $(BASE_BIN_DIR)/herv_adjacent_comparison.sh
# rm -f $(BASE_BIN_DIR)/herv_k113_integration.sh
# rm -f $(BASE_BIN_DIR)/herv_trim_comparison.sh
# rm -f $(BASE_BIN_DIR)/human_genomic_fasta_to_bowtie_index.sh
# rm -f $(BASE_BIN_DIR)/insertion_points_to_table.sh
# rm -f $(BASE_BIN_DIR)/just_first_contig_match_results.rb
# rm -f $(BASE_BIN_DIR)/lines_not_in_reference_list.sh
# rm -f $(BASE_BIN_DIR)/modify_trinity_output.pl
# rm -f $(BASE_BIN_DIR)/overlapper_insertion_points_to_fasta.sh
# rm -f $(BASE_BIN_DIR)/overlapper_seeker.sh
# rm -f $(BASE_BIN_DIR)/overlappers_reference_to_table.sh
# rm -f $(BASE_BIN_DIR)/overlappers_to_table.sh
# rm -f $(BASE_BIN_DIR)/pieces_check.sh
# rm -f $(BASE_BIN_DIR)/pieces_merge.sh
# rm -f $(BASE_BIN_DIR)/positions_within_10bp.sh
# rm -f $(BASE_BIN_DIR)/positions_within_10bp_of_reference.sh
# rm -f $(BASE_BIN_DIR)/pull_reads_fasta.pl
# rm -f $(BASE_BIN_DIR)/pull_reads_fasta.rb
# rm -f $(BASE_BIN_DIR)/quick_dark.sh
# rm -f $(BASE_BIN_DIR)/remove_N_reads_from_fasta.awk
# rm -f $(BASE_BIN_DIR)/remove_N_reads_from_fasta.sh
# rm -f $(BASE_BIN_DIR)/remove_human_with_bowtie2.sh
# rm -f $(BASE_BIN_DIR)/rins.pl
# rm -f $(BASE_BIN_DIR)/rins.rb
# rm -f $(BASE_BIN_DIR)/rins_ccls_lib.rb
# rm -f $(BASE_BIN_DIR)/sam2names.pl
# rm -f $(BASE_BIN_DIR)/sam2names.rb
# rm -f $(BASE_BIN_DIR)/sam_to_bam.sh
# rm -f $(BASE_BIN_DIR)/samtools_bam_to_fasta.sh
# rm -f $(BASE_BIN_DIR)/samtools_bam_to_paired_fastq.sh
# rm -f $(BASE_BIN_DIR)/samtools_depth_comparison.sh
# rm -f $(BASE_BIN_DIR)/samtools_extract_aligned_reads.sh
# rm -f $(BASE_BIN_DIR)/samtools_extract_and_clip_chimeric_reads.sh
# rm -f $(BASE_BIN_DIR)/samtools_extract_half_mapped_pairs.sh
# rm -f $(BASE_BIN_DIR)/select_no_hits_from_blast.awk
# rm -f $(BASE_BIN_DIR)/select_no_hits_from_blast.sh
# rm -f $(BASE_BIN_DIR)/sequencing_lib.rb
# rm -f $(BASE_BIN_DIR)/simple_queue.sh
# rm -f $(BASE_BIN_DIR)/simple_queue_cron.sh
# rm -f $(BASE_BIN_DIR)/simple_queue_eval.sh
# rm -f $(BASE_BIN_DIR)/simple_queue_pop_to_script.sh
# rm -f $(BASE_BIN_DIR)/spacify_sequence_names.rb
# rm -f $(BASE_BIN_DIR)/srun_bam2fastx_fastq.sh
# rm -f $(BASE_BIN_DIR)/srun_blast.sh
# rm -f $(BASE_BIN_DIR)/srun_blastn_to_nt.sh
# rm -f $(BASE_BIN_DIR)/srun_bowtie2.sh
# rm -f $(BASE_BIN_DIR)/srun_ec_quick_dark.sh
# rm -f $(BASE_BIN_DIR)/srun_fastq_to_fasta.sh
# rm -f $(BASE_BIN_DIR)/srun_fastx_collapser.sh
# rm -f $(BASE_BIN_DIR)/srun_gunzip.sh
# rm -f $(BASE_BIN_DIR)/srun_herv_k113_integration.sh
# rm -f $(BASE_BIN_DIR)/srun_lane_fastq.sh
# rm -f $(BASE_BIN_DIR)/srun_overlapper_seeker.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_bam2fq.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_bam_to_paired_fastq.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_depth_comparison.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_extract_aligned_reads.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_extract_and_clip_chimeric_reads.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_extract_half_mapped_pairs.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_sam_to_bam.sh
# rm -f $(BASE_BIN_DIR)/srun_samtools_sort_bam_by_name.sh
# rm -f $(BASE_BIN_DIR)/srun_trinity.sh
# rm -f $(BASE_BIN_DIR)/to_table.gawk
# rm -f $(BASE_BIN_DIR)/trim_alignments_and_descriptions.awk
# rm -f $(BASE_BIN_DIR)/trim_alignments_and_descriptions.sh
# rm -f $(BASE_BIN_DIR)/underscore_sequence_names.rb
# rm -f $(BASE_BIN_DIR)/uniquify_sequence_names.rb
# rm -f $(BASE_BIN_DIR)/write_result.pl
# rm -f $(BASE_BIN_DIR)/write_result.rb
uninstall: uninstall-scripts
uninstall-scripts:
@printf "\nUNINSTALLING SCRIPTS\n\n"
cd $(BASE_BIN_DIR); \
find . -lname $(APPS_SUBDIR)/\* -exec rm {} \;
rm -rf $(BASE_BIN_DIR)/$(APPS_SUBDIR)
# Don't know why I have the "-depth 1" here? Won't work on ec2 instance.
# find . -lname $(APPS_SUBDIR)/\* -depth 1 -exec rm {} \;
#$ find . -lname ccls_sequencing/\* -depth 1
#find: warning: you have specified the -depth option after a non-option argument -lname, but options are not positional (-depth affects tests specified before it as well as those specified after it). Please specify options before other arguments.
#
#find: paths must precede expression: 1
#Usage: find [-H] [-L] [-P] [-Olevel] [-D help|tree|search|stat|rates|opt|exec] [path...] [expression]
# Remove old stuff. Need -f or get an error.
install-scripts: uninstall-scripts
$(MKDIR) $(BASE_BIN_DIR)/$(APPS_SUBDIR)
@printf "\nINSTALLING SCRIPTS\n\n"
cp rins_ccls/*.gawk $(BASE_BIN_DIR)/$(APPS_SUBDIR)/
cp rins_ccls/*.awk $(BASE_BIN_DIR)/$(APPS_SUBDIR)/
cp rins_ccls/*.pl $(BASE_BIN_DIR)/$(APPS_SUBDIR)/
cp rins_ccls/*.rb $(BASE_BIN_DIR)/$(APPS_SUBDIR)/
cp rins_ccls/*.sh $(BASE_BIN_DIR)/$(APPS_SUBDIR)/
cd $(BASE_BIN_DIR); \
for file in `find $(APPS_SUBDIR) -type f` ; do \
echo $$file; \
ln -s $$file; \
done
# cp rins_ccls/*awk $(BASE_BIN_DIR)
# *awk would include *.awk and *.gawk
# using latest trinity which DOES not need this
# cp SAM_filter_out_unmapped_reads.pl $(BASE_BIN_DIR)/util/
#clean: clean_blat clean_bwa clean_trinity clean_price
#clean: clean_blat clean_bwa clean_price
clean: clean-all $(TARGETS:%=clean-%)
@printf "\nDONE CLEANING\n\n"
clean-all:
@printf "\nCLEANING ALL\n\n"
# rins nothing to clean
# ccls nothing to clean
#blat:
# @printf "\nMAKING BLAT\n\n"
# cd $(BLAT) && $(MKDIR) bin && make C_INCLUDE_PATH=/opt/local/include/ PNGLIB=/opt/local/lib/libpng.a BINDIR=`pwd`/bin
#
#install-blat:
# @printf "\nINSTALLING BLAT\n\n"
# cp $(BLAT)/bin/* $(BASE_BIN_DIR)
#
#clean-blat:
# @printf "\nCLEANING BLAT\n\n"
# cd $(BLAT) && make clean && rm -f */*/*.a
#bowtie:
# @printf "\nMAKING BOWTIE\n\n"
# cd $(BOWTIE) && make
#
#install-bowtie:
# @printf "\nINSTALLING BOWTIE\n\n"
# cd $(BOWTIE) && cp bowtie bowtie-build bowtie-inspect $(BASE_BIN_DIR)
#
#clean-bowtie:
# @printf "\nCLEANING BOWTIE\n\n"
# cd $(BOWTIE) && make clean
bowtie2:
@printf "\nMAKING BOWTIE2\n\n"
cd $(BOWTIE2) && make
install-bowtie2:
@printf "\nINSTALLING BOWTIE2\n\n"
cd $(BOWTIE2) && cp bowtie2 bowtie2-build bowtie2-align bowtie2-inspect $(BASE_BIN_DIR)
clean-bowtie2:
@printf "\nCLEANING BOWTIE2\n\n"
cd $(BOWTIE2) && make clean
#blast:
# @printf "\nMAKING BLAST\n\n"
## Use BASE_DIR as blast creates bin/, lib/ and include/
# cd $(BLAST) && ./configure --prefix=$(BASE_DIR) && make
#
#install-blast:
# @printf "\nINSTALLING BLAST\n\n"
# cd $(BLAST) && make install
#
#clean-blast:
# @printf "\nCLEANING BLAST\n\n"
# /bin/rm -rf $(BLAST)/*-Debug*
#
#trinity:
# @printf "\nMAKING TRINITY\n\n"
# cd $(TRINITY) && make
#
#install-trinity:
# @printf "\nINSTALLING TRINITY\n\n"
## this works, but copies too much
## cp -r $(TRINITY)/* $(BASE_BIN_DIR)
## These more explicit copies still copy too much, and the links
## considering using "cp -R" which will preserve the links
## cp -r $(TRINITY)/Analysis $(BASE_BIN_DIR)
## cp -r $(TRINITY)/Butterfly $(BASE_BIN_DIR)
## cp -r $(TRINITY)/Chrysalis $(BASE_BIN_DIR)
## cp -r $(TRINITY)/Inchworm $(BASE_BIN_DIR)
## cp -r $(TRINITY)/PerlLib $(BASE_BIN_DIR)
## cp -r $(TRINITY)/PerlLibAdaptors $(BASE_BIN_DIR)
## cp -r $(TRINITY)/Trinity.pl $(BASE_BIN_DIR)
## cp -r $(TRINITY)/trinity-plugins $(BASE_BIN_DIR)
## cp -r $(TRINITY)/util $(BASE_BIN_DIR)
## I highly recommend that you just add the trinity root directory to the PATH
#
#clean-trinity:
# @printf "\nCLEANING TRINITY\n\n"
# cd $(TRINITY) && make clean
#
##LICENSE
##Makefile
##README
##Release.Notes
##docs
##misc
##notes
#
#rins:
# @printf "\nMAKING RINS WOULD BE NICE, BUT JUST SCRIPTS\n\n"
#
#ccls:
# @printf "\nMAKING CCLS WOULD BE NICE, BUT JUST SCRIPTS\n\n"
bwa:
@printf "\nMAKING BWA\n\n"
cd $(BWA) && make
install-bwa:
@printf "\nINSTALLING BWA\n\n"
cp $(BWA)/bwa $(BASE_BIN_DIR)
clean-bwa:
@printf "\nCLEANING BWA\n\n"
cd $(BWA) && make clean
price:
@printf "\nMAKING PRICE\n\n"
cd $(PRICE) && make
install-price:
@printf "\nINSTALLING PRICE\n\n"
cp $(PRICE)/PriceTI $(BASE_BIN_DIR)
clean-price:
@printf "\nCLEANING PRICE\n\n"
cd $(PRICE) && make clean
# The dir name is ray so 'make ray' will not run.
.PHONY: ray
ray:
@printf "\nMAKING RAY\n\n"
cd $(RAY) && make
install-ray:
@printf "\nINSTALLING RAY\n\n"
cp $(RAY)/Ray $(BASE_BIN_DIR)
clean-ray:
@printf "\nCLEANING RAY\n\n"
cd $(RAY) && make clean
velvet:
@printf "\nMAKING VELVET\n\n"
cd $(VELVET) && make
install-velvet:
@printf "\nINSTALLING VELVET\n\n"
cp $(VELVET)/velvet? $(BASE_BIN_DIR)
clean-velvet:
@printf "\nCLEANING VELVET\n\n"
cd $(VELVET) && make clean
test:
@printf "\ntesting is nice, but not today\n\n"
# cd $(BLAT) && make test
# cd $(BLAST) && make test
# cd $(BOWTIE) && make test
# cd $(BOWTIE2) && make test
# cd $(TRINITY) && make test
# rins
# ccls