* turns out test data project_df.csv was hard-wired to paths on marga…

…ret. Modified to be relative to spacemake source

test_data/test_project_df.csv

@@ -1,8 +1,8 @@
 project_id,sample_id,puck_barcode_file_id,sample_sheet,species,demux_barcode_mismatch,demux_dir,basecalls_dir,R1,R2,reads,longreads,longread_signature,investigator,sequencing_date,experiment,puck_barcode_file,run_mode,barcode_flavor,is_merged,merged_from,puck,dge,map_strategy,adapter_flavor
-test,test_01,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
-test,test_01b,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
-test,test_02,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
-test,test_03_nofinal,['no_spatial_data'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR,dropseq
-tile,tile_1,['tile_1'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_1.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
-tile,tile_2,['tile_2'],,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_2.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
-tile,tile_both,"['tile_1', 'tile_2']",,test_hsa,1,,,['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R1.fastq.gz'],['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,"['/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_1.txt', '/data/local/rajewsky/home/marjens/git/spacemake/spacemake/../test_data/tile_2.txt']",['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
+test,test_01,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
+test,test_01b,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,STAR:genome,dropseq
+test,test_02,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
+test,test_03_nofinal,['no_spatial_data'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,,['default'],dropseq,False,[],default,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR,dropseq
+tile,tile_1,['tile_1'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['{spacemake_dir}/test_data/tile_1.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
+tile,tile_2,['tile_2'],,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,['{spacemake_dir}/test_data/tile_2.txt'],['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq
+tile,tile_both,"['tile_1', 'tile_2']",,test_hsa,1,,,['{spacemake_dir}/test_data/reads_chr22_R1.fastq.gz'],['{spacemake_dir}/test_data/reads_chr22_R2.fastq.gz'],,,,unknown,unknown,unknown,"['{spacemake_dir}/test_data/tile_1.txt', '{spacemake_dir}/test_data/tile_2.txt']",['spatial_rm'],dropseq,False,[],test_puck,,rRNA:bowtie2->miRNA:bowtie2->genome:STAR:final,dropseq

tests/fixtures.py

@@ -2,6 +2,7 @@
 import os
 
 spacemake_dir = os.path.abspath(os.path.dirname(__file__) + '/../')
+print("SPACEMAKE_DIR", spacemake_dir)
 
 def sm(*argc, expect_fail=False):
     # construct the desired cmdline
@@ -120,7 +121,10 @@ def configured_root(tmp_path_factory):
     os.system(f"cp {def_config} {tmp_root / 'config.yaml'}")
 
     test_pdf =  os.path.join(sm_path, "../test_data/test_project_df.csv")
-    os.system(f"cp {test_pdf} {tmp_root / 'project_df.csv'}")
+    open(f"{tmp_root / 'project_df.csv'}", 'w').write(
+        open(test_pdf, 'r').read().format(spacemake_dir=spacemake_dir)
+    )
+    #os.system(f"cp {test_pdf} {tmp_root / 'project_df.csv'}")
 
     return tmp_root