No rule to make target

[sb43]

@nunofonseca I am getting following error when trying to run latest docker version of irap: Would you please help to debug the issue, thanks, Shriram ubuntu@f852531d9786:/mymount$ irap conf=myirp.cfg

---

• IRAP 1.0.0b
• Developed by Nuno Fonseca (authorname (at) acm.org)
• This pipeline is distributed under the terms of the GNU General Public License 3
• Initializing...
• Trying to load configuration file myirp.cfg...
• Configuration loaded.
• atlas_run mode (overriding some options)
• sop=atlas (using pre-defined SOP, overriding some options)
• SOP=Expression Atlas
• Required Parameters:
• name=HSC-4_RNA_TCGA_e77
• data_dir=irap_data
• species=human
• raw_data_dir=irap_data/raw_data/HSC-4_RNA_TCGA_e77_human/
• reference=Homo_sapiens.GRCh38.dna.toplevel.fa.gz
• gtf_file = Homo_sapiens.GRCh38.79.gtf.gz
• Transcripts = /mymount/irap_data/reference/human/Homo_sapiens.GRCh38.dna.toplevel.cdna.all.fa
• gff3_file = HSC-4_RNA_TCGA_e77/data/Homo_sapiens.GRCh38.79.gff3
• Validating se and pe
• pe parameter or se parameter should be defined and non-empty
• groups= parameter not defined, this should be defined if you intend to generate an HTML report for the inferred gene/level/transcript quantification
• technical_replicates=NONE
• Optional Parameters:
• rnaseq_type=blk
• max_threads=8
• tmp_dir=irap_data/tmp (temporary directory)
• qc/filter=on
• mapper=tophat2
• quant_method=htseq2
• exon_quant=y
• exon_quant_method=dexseq
• transcript_quant=n
• transcript_expr=n
• quant_norm_tool=irap
• quant_norm_method=tpm
• quant_norm_mass_biotypes=
• mapper_splicing=yes
• de_method=deseq2
• de_pvalue_cutoff=0.05
• transcript_de_method=none
• transcript_de_pvalue_cutoff=0.05
• exon_de_method=none
• exon_de_pvalue_cutoff=0.05 bash: bc: command not found
• barcode_post_process_bam=n
• gse_tool=none
• Atlas mode enabled % YAP execution halted *========================================================

• Files/folders: Top level folder: HSC-4_RNA_TCGA_e77 Aux data: HSC-4_RNA_TCGA_e77/data QC for input files: HSC-4_RNA_TCGA_e77/irap_qc Alignment files: HSC-4_RNA_TCGA_e77/irap_qc/tophat2 Quantification matrices: HSC-4_RNA_TCGA_e77/irap_qc/tophat2/htseq2 Gene level DE: HSC-4_RNA_TCGA_e77/irap_qc/tophat2/htseq2/deseq2

• 29/11/2018 15:26:04 : [DONE] Initialization
• 29/11/2018 15:26:04 : [DONE] Directory structure created make: *** No rule to make target '/mymount/irap_data/reference/human/Homo_sapiens.GRCh38.dna.toplevel.cdna.all.fa', needed by 'setup_files'. Stop

[sb43]

Thanks @nunofonseca issue is resolved after applying your suggestion of copying Homo_sapiens.GRCh38.79.cdna.all.fa(.gz) to "/mymount/irap_data/reference/human/ "