diff --git a/README.md b/README.md index 878fe5f162e7b6da2c37b3fb2de9f297778549ac..7a6343fa29335b865c7a5cde87056a9934162cdb 100644 --- a/README.md +++ b/README.md @@ -48,6 +48,7 @@ Directory |Â Purpose ## Bumping to ARC v1.1 (23.03.2022) +### by arcCommander / shell > depends on arcCommander v3 or higher ```bash @@ -61,4 +62,33 @@ arc study add -s TalinumGenomeDraft # add draft genome as study mv externals/Talinum.gm.CDS.nt.fa studies/TalinumGenomeDraft/resources # mv genome to resources rm -r externals rm inv.json + +arc assay register -s TalinumFacultativeCAM -a Talinum_RNASeq_minimal # re-register assay +arc update + +mv assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md studies/TalinumFacultativeCAM/protocols # move plant growth from assay to study + +arc assay remove -s TalinumFacultativeCAM -a RNASeq_Kallisto_quant # add computational parts as assay + +``` + +> note: soft assay + +### by hand +- move plant growth sheet isa.assay to isa.study +- remove computational RNASeq sheet from assays as it partly duplicates the (not yet CWLed) kallisto workflow + +### add placeholder sample descriptors + +```bash +arc_root=$(pwd) +cd studies/TalinumFacultativeCAM/resources/ +touch \ +DB_097 \ +DB_099 \ +DB_103 \ +DB_161 \ +DB_163 \ +DB_165 +cd $arc_root ``` \ No newline at end of file diff --git a/assays/Talinum_RNASeq_minimal/isa.assay.xlsx b/assays/Talinum_RNASeq_minimal/isa.assay.xlsx index f91d272bc63f657deb87140a6ecfa5fc2a551847..3e2dc03464a66d388eeb2dd3b6aafe7f8ca214b0 100644 Binary files a/assays/Talinum_RNASeq_minimal/isa.assay.xlsx and b/assays/Talinum_RNASeq_minimal/isa.assay.xlsx differ diff --git a/isa.investigation.xlsx b/isa.investigation.xlsx index dde03a8bf2dd4e29ec9a0e45060f705aa5872340..4534a8f94f71621972ef05ce76bb33700285cfe2 100644 Binary files a/isa.investigation.xlsx and b/isa.investigation.xlsx differ diff --git a/studies/TalinumFacultativeCAM/isa.study.xlsx b/studies/TalinumFacultativeCAM/isa.study.xlsx index 3f7f18c21be63d7dbd5ca2dee5fe162fae75d4d8..9626ca8dbb0a9077075e18bf3cd07b9440da2b53 100644 Binary files a/studies/TalinumFacultativeCAM/isa.study.xlsx and b/studies/TalinumFacultativeCAM/isa.study.xlsx differ diff --git a/studies/TalinumFacultativeCAM/old.study.xlsx b/studies/TalinumFacultativeCAM/old.study.xlsx deleted file mode 100644 index 3dc159704211be4bd2b6d62bfc315a48f567e134..0000000000000000000000000000000000000000 Binary files a/studies/TalinumFacultativeCAM/old.study.xlsx and /dev/null differ diff --git a/assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md b/studies/TalinumFacultativeCAM/protocols/01_plant_material.md similarity index 100% rename from assays/Talinum_RNASeq_minimal/protocols/01_plant_material.md rename to studies/TalinumFacultativeCAM/protocols/01_plant_material.md diff --git a/studies/TalinumFacultativeCAM/resources/DB_097 b/studies/TalinumFacultativeCAM/resources/DB_097 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/TalinumFacultativeCAM/resources/DB_099 b/studies/TalinumFacultativeCAM/resources/DB_099 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/TalinumFacultativeCAM/resources/DB_103 b/studies/TalinumFacultativeCAM/resources/DB_103 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/TalinumFacultativeCAM/resources/DB_161 b/studies/TalinumFacultativeCAM/resources/DB_161 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/TalinumFacultativeCAM/resources/DB_163 b/studies/TalinumFacultativeCAM/resources/DB_163 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/studies/TalinumFacultativeCAM/resources/DB_165 b/studies/TalinumFacultativeCAM/resources/DB_165 new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391