Symlink *.loc.sample files to have one master copy of each

[peterjc]

We have multiple copies of many *.loc.sample files, for example in a data manager and in tools which use those files. Keeping their internal documentation in sync would be easier if there was a master copy (e.g. under the repository in a top level folder loc_files/) and everything else was a symlink to this.

$ find . -type f -name *.loc.sample | rev | cut -d "/" -f 1 | rev | sort | uniq -c | sort -n -r
     30 all_fasta.loc.sample
     12 fasta_indexes.loc.sample
      4 gene_sets.loc.sample
      3 metaphlan2_database.loc.sample
      3 kraken_databases.loc.sample
      2 twobit.loc.sample
      2 snpsift_dbnsfps.loc.sample
      2 snpsift_dbnsfp.loc.sample
      2 snpeffv_regulationdb.loc.sample
      2 snpeffv_genomedb.loc.sample
      2 sam_fa_indices.loc.sample
      2 rnastar_index2.loc.sample
      2 qiime_trees.loc.sample
      2 qiime_taxonomy.loc.sample
      2 qiime_rep_set.loc.sample
      2 qiime_rep_set_aligned.loc.sample
      2 picard_index.loc.sample
      2 mothur_taxonomy.loc.sample
      2 mothur_map.loc.sample
      2 mothur_lookup.loc.sample
      2 mothur_aligndb.loc.sample
      2 lastz_seqs.loc.sample
      2 kallisto_indexes.loc.sample
      2 humann2_protein_database.loc.sample
      2 humann2_nucleotide_database.loc.sample
      2 hisat2_indexes.loc.sample
      2 gemini_databases.loc.sample
      2 dbkeys.loc.sample
      2 bwameth_indexes.loc.sample
      2 bwa_mem_index.loc.sample
      2 busco.loc.sample
      2 bowtie2_indices.loc.sample
      1 tophat2_indices.loc.sample
      1 snpeffv_databases.loc.sample
      1 snpeff_msigdb_database.loc.sample
      1 plant_tribes_scaffolds.loc.sample
      1 picrust_precalculated.loc.sample
      1 ncbi_taxonomy.loc.sample
      1 meme_motif_databases.loc.sample
      1 liftOver.loc.sample
      1 hmm_database.loc.sample
      1 gene_annotation.loc.sample
      1 gatk_sorted_picard_index.loc.sample
      1 gatk2_picard_index.loc.sample
      1 featurecounts_anno.loc.sample
      1 bowtie_indices.loc.sample
      1 bowtie_indices_color.loc.sample
      1 blastdb_p.loc.sample
      1 all_gff.loc.sample
      1 alignseq.loc.sample
      1 adapters.loc.sample

Looking at all_fasta.loc.sample which appears 30 times, these files have lots of different versions,

$ md5sum $(find . -name all_fasta.loc.sample)
6b6fe23b090014dd50249e3c51e09c21  ./data_managers/data_manager_hisat2_index_builder/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./data_managers/data_manager_bowtie_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_twobit_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_bwameth_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_picard_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_fetch_genome_dbkeys_all_fasta/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_gatk_picard_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_bwa_mem_index_builder/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./data_managers/data_manager_kallisto_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_sam_fasta_index_builder/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./data_managers/data_manager_star_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./data_managers/data_manager_bowtie2_index_builder/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./tools/fermikit/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/bedtools/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/exonerate/tool-data/all_fasta.loc.sample
195763f15417173307d9d1a5075a1643  ./tools/multigps/tool-data/all_fasta.loc.sample
c52f2164597499a7aa92872cdcd72c43  ./tools/ucsc_blat/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/meme/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/star_fusion/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/pilon/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./tools/circos/tool-data/all_fasta.loc.sample
97122de7c46b3c9e90fb9f9dea50d4e9  ./tools/scpipe/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/transtermhp/all_fasta.loc.sample
97122de7c46b3c9e90fb9f9dea50d4e9  ./tools/pizzly/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/jcvi_gff_stats/tool-data/all_fasta.loc.sample
25af1f4351cc8ba451051f731fd3dcc6  ./tools/length_and_gc_content/tool-data/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/jbrowse/tool-data/all_fasta.loc.sample
fbbecafba7191825d29a765f52975839  ./tools/jbrowse/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/minimap2/all_fasta.loc.sample
6b6fe23b090014dd50249e3c51e09c21  ./tools/crossmap/tool-data/all_fasta.loc.sample

See also #2082 noting some of the sample files are empty.