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File Rev. Age Author Last log entry
 Parent Directory        
ExpandSims.pm  1.1  11 years  olson  initial checking of metagenome 48 stuff
MGDB.pm  1.2  10 years  olson  use INTEGER instead of SMALLINT for contig offsets.
Makefile  1.17  8 years  dsouza  Added mg_create_histogram_images.pl
README  1.2  10 years  olson  Development checkin of new metagenomics RAST pipeline.
SimDB.pm  1.3  9 years  redwards  methods for getting upgrades between databases
SimStatusDB.pm  1.3  10 years  olson  Add connect/disconnect to SimStatusDB. Disconnect while sims run.
TaxStr.pm  1.2  10 years  olson  Development checkin of new metagenomics RAST pipeline.
check_jobs_mg.pl  1.18  10 years  olson  add mgrast2 check
copy_metagenome.pl  1.1  9 years  redwards  code to copy a v1 metagenome to a new job
find_broken_jobs.pl  1.1  10 years  olson  Development checkin of new metagenomics RAST pipeline.
find_jobs_with_short_seqs.pl  1.1  10 years  olson  Development checkin of new metagenomics RAST pipeline.
finish_job.pl  1.2  9 years  redwards  changing the user object accessors
format_all_public_metagenomes.pl  1.1  9 years  redwards  code to format all public metagenome contigs files
get_sim_status.pl  1.3  9 years  redwards  changing the user object accessors
load_sim_data.pl  1.4  10 years  olson  Loader tweaks.
load_sim_data_noncached.pl  1.1  10 years  olson  Rename sim data loader scripts.
load_tax.pl  1.3  10 years  olson  Updates to mgrast sim loader.
merge_repaired_job_results.pl  1.1  10 years  olson  Development checkin of new metagenomics RAST pipeline.
mg_check_sims.pl  1.5  8 years  dsouza  Set status for a load at the same time the sge job is created
mg_chunk_sims.pl  1.2  10 years  olson  Development checkin of new metagenomics RAST pipeline.
mg_compute_sims.pl  1.5  10 years  olson  Add connect/disconnect to SimStatusDB. Disconnect while sims run.
mg_compute_sims_on_timelogic.pl  1.9  11 years  mkubal  -priority 5, records SOC job to meta.xml
mg_create_db_indexes.pl  1.1  10 years  olson  Commit of initial MGRAST2 code.
mg_create_histogram_images.pl  1.2  8 years  dsouza  removed comments
mg_create_seed_org.pl  1.4  8 years  dsouza  stripped down to bare essentials -- create a directory, rewrite the sequence fil...
mg_export.pl  1.3  8 years  dsouza  Rewritten to export to genbank using database tables, creates rp directory and e...
mg_figfam.pl  1.2  11 years  olson  Some minor mg assignment fixes
mg_gen_subsystem_tax.pl  1.1  10 years  olson  Development checkin of new metagenomics RAST pipeline.
mg_load_done.pl  1.3  10 years  olson  Replace the MLDBM/DB_File sim status database with a postgres version.
mg_load_sims.pl  1.3  10 years  olson  Replace the MLDBM/DB_File sim status database with a postgres version.
mg_load_sims_file.pl  1.3  9 years  jared  Disabled full sims table load
mg_load_tax_db.pl  1.2  10 years  olson  Commit of initial MGRAST2 code.
mg_norm_16s.pl  1.1  10 years  olson  Commit of initial MGRAST2 code.
mg_norm_euro.pl  1.1  10 years  olson  Commit of initial MGRAST2 code.
mg_norm_greengenes.pl  1.1  10 years  olson  Commit of initial MGRAST2 code.
mg_norm_silva.pl  1.1  10 years  olson  Development checkin of new metagenomics RAST pipeline.
mg_port_job.pl  1.2  10 years  olson  die if job already loaded
mg_postproc_taxa_sims.pl  1.13  10 years  olson  Development checkin of new metagenomics RAST pipeline.
mg_preprocess.pl  1.18  10 years  arodri7  update the metagene process tool
mg_sims.pl  1.12  10 years  dsouza  Changed job priority to low (in sge queue)
mg_sims_done.pl  1.1  11 years  olson  initial checking of metagenome 48 stuff
mg_sims_to_gff_and_gbk.pl  1.3  9 years  dsouza  Changed from using system call to pipe to gzip in filehandle to zip file
mg_to_gbk.pl  1.4  9 years  dsouza  set meta status to error if gff required and not found, cleaned out junk
mg_upgrade_preprocess.pl  1.1  9 years  redwards  two parts of the code for upgrading from an old version of mg-rast to a newer ve...
mg_upgrade_sims.pl  1.1  9 years  redwards  two parts of the code for upgrading from an old version of mg-rast to a newer ve...
pull_sge_accounting_for_jobs.pl  1.1  10 years  olson  Development checkin of new metagenomics RAST pipeline.
recover_broken_job.pl  1.6  9 years  redwards  updating with new databases
reload_job_sims.pl  1.1  10 years  olson  script to reload all sims for a mgrast job.
remake_sims_tables.pl  1.1  10 years  olson  Rebuild a job's database tables .
renumber_split_move_blastx.pl  1.1  10 years  redwards  Process and consume externally ran blastx jobs into the mg-rast pipeline
reset_sims_load.pl  1.1  9 years  redwards  code to reset lost mg sims loading
resume_after_fixed_fasta.pl  1.2  10 years  redwards  just adding a test that the file was found
summarize_mgrast_taxa.pl  1.1  11 years  olson  Summarize all taxa info for all jobs in the mgrast.
tax-schema.sql  1.4  10 years  olson  Commit of initial MGRAST2 code.

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