RAPT v0.5.1 - teamcity CI

GCP RAPT.md

@@ -20,7 +20,7 @@ Here are instructions to execute RAPT once your system is set up. Additional ins
 3.	Download the latest release by executing the following commands:
 
     ```
-    ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v1.2.2/rapt-v1.2.2.tar.gz
+    ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.1/rapt-v0.5.1.tar.gz
     ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
     ```
 4.	Run `run_rapt_gcp.sh help` to see the *GCP RAPT* usage information.

README.md

@@ -2,17 +2,17 @@
 
 RAPT is a NCBI pipeline designed for assembling and annotating short genomic sequencing reads obtained from bacterial or archaeal isolates. RAPT consists of two major components, [SKESA](https://github.com/ncbi/SKESA) and [PGAP](https://github.com/ncbi/pgap). SKESA is a *de novo* assembler for microbial genomes based on DeBruijn graphs. PGAP is a prokaryotic genome annotation pipeline that combines *ab initio* gene prediction algorithms with homology-based methods. RAPT takes an SRA run or a fasta or fastq file of Illumina reads as input and produces an assembled and annotated genome. 
 
-If you are new to RAPT, please visit our [wiki page](https://github.com/ncbi/rapt/wiki) for detailed information.
+If you are new to RAPT, please visit our [wiki page](https://github.com/ncbi/rapt/wiki) for detailed information, and watch a [short webinar](https://www.youtube.com/watch?v=7trM1pKAVXQ).
 
-![RAPT](RAPT_context2.png)
+![RAPT](RAPT_context4.png)
 
 To use the latest version, download the RAPT command-line interface with the following commands:
 ```
-~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v1.2.2/rapt-v1.2.2.tar.gz
+~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.1/rapt-v0.5.1.tar.gz
 ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
 ```
 
 
-There should be two scripts in your directory now, `run_rapt_gcp.sh` and `run_rapt.py`, corresponding to two variations of RAPT:  Google Cloud Platform (GCP) RAPT and Standalone RAPT. [GCP RAPT](GCP%20RAPT.md) is designed to run on GCP and is for users with GCP accounts (please note this is different from a gmail account), while [Stand-alone RAPT](Standalone%20RAPT.md) can run on any computing environments meeting a few pre-requisites.
+There should be two scripts in your directory now, `run_rapt_gcp.sh` and `run_rapt.py`, corresponding to two variations of RAPT:  Google Cloud Platform (GCP) RAPT and Standalone RAPT. [GCP RAPT](https://github.com/ncbi/rapt/wiki/GCP%20RAPT%20In-depth%20Documentation%20and%20Examples) is designed to run on GCP and is for users with GCP accounts (please note this is different from a gmail account), while [Stand-alone RAPT](https://github.com/ncbi/rapt/wiki/Standalone%20RAPT%20In-depth%20Documentation%20and%20Recommendations) can run on any computing environments meeting a few pre-requisites.
 
-For instructions on running RAPT, please go to their respective documentation pages: [GCP RAPT](GCP%20RAPT.md) or [Stand-alone RAPT](Standalone%20RAPT.md).
+For instructions on running RAPT, please go to their respective documentation pages: [GCP RAPT](https://github.com/ncbi/rapt/wiki/GCP%20RAPT%20In-depth%20Documentation%20and%20Examples) or [Stand-alone RAPT](https://github.com/ncbi/rapt/wiki/Standalone%20RAPT%20In-depth%20Documentation%20and%20Recommendations).

Standalone RAPT.md

@@ -31,7 +31,7 @@ Here are instructions to execute RAPT once your system is set up. Additional ins
 2. Download the latest release by executing the following commands:<br>
 
     ```
-    ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v1.2.2/rapt-v1.2.2.tar.gz
+    ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.1/rapt-v0.5.1.tar.gz
     ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
     ```
 3. Run `./run_rapt.py -h` to see the *Stand-alone RAPT* usage information<br>

dist/CHANGELOG.md

@@ -1,4 +1,53 @@
-### Release v1.2.2
+### Release v0.5.1
+* PGAP at 2022-02-10.build5872
+
+### Release v0.5.0
+- updated PGAPX to 2021-11-29.build574
+- use dedicated ```prefetch``` binary instead of curl to retrieve SRA data
+
+
+### Release v0.4.2
+- upgrade to booster 1.76 for SKESA
+
+### Release v0.4.1
+* Fix double quoted string syntax error
+* try use fewer words of genus_species string and retry if taxcheck fails
+* try to run GCP RAPT even if network connection detection failed.
+
+### Release v0.4.0
+* Update SKESA to 2.5.0 and PGAPX to 2021-07-01.build5508
+* Remove container upon exit with '--rm' (docker and podman)
+* Refactoring to use config loader
+* Download reference data from Google storage if run on GCP (run_rapt_gcp.sh)
+* Improved organism name parsing algorithm
+* Distinguish different flavors of RAPT in applog
+* Some bug fixes
+
+### Release v0.3.2
+- change default machine type from n1-himem-16 to n1-himem-8
+- attach ncbi_user to pinger events if run by web-rapt
+
+### Release v0.3.1
+- Added --network command line to specify custom network for container
+- Some exit codes merged and combined
+- Exclude dummy strings for taxonomy names
+- Remove redundent errors.xml file from pgap output
+- Updated SKESA version and ngs/vdb libs
+- Added docker daemon status check
+
+### Release v0.3.0
+- new PGAP version
+- sends email notifications
+- accepts forward and reverse reads in two files
+- monitors user quotas
+- verifies taxonomic data
+- accepts an argument to stop upon taxonomic disagreement
+- bug fixes, including invalid SRA index
+- improved logging
+- improved error messaging
+- cleaned up output files
+
+### Release v2.2.6
  - GCP-RAPT: added `--project` option to specify custom project.
  - GCP-RAPT: log file names are fixed to concise.log and verbose.log
  - GCP-RAPT: log files are included in the output archive

dist/README.txt

@@ -1,4 +1,4 @@
-Read Assembly and Annotation Pipeline Tool (RAPT) v1.2.2
+Read Assembly and Annotation Pipeline Tool (RAPT) v0.5.1
 
 RAPT is a NCBI pipeline designed for assembling and annotating Illumina genome sequencing reads obtained from bacterial or archaeal isolates. RAPT consists of two major NCBI components, SKESA and PGAP. SKESA is a de-novo assembler for microbial genomes based on DeBruijn graphs. PGAP is a prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. RAPT takes an Illumina SRA run or a fasta file as input and produces an assembled and annotated genome. 
 

dist/release-notes.txt

@@ -1,12 +1,9 @@
-RELEASE: v1.2.2
-DATE: 12-29-2020
-BUILD: rapt-30372431
-SKESA: 2.4.0
-PGAPX: 2020-09-24.build4894
+RELEASE: v0.5.1
+DATE: 03-18-2022
+BUILD: rapt-37347638
+SKESA: 2.5.0
+PGAPX: 2022-02-10.build5872
 
 DESCRIPTION:
 
-DESCRIPTION:
-	GCP-RAPT now displays job status in "joblist" command as "Done" and "Failed" instead of "Finished" and "Aborted" for more clarity; and more information has been added to the output of "jobdetails" command for easier problem identification. Log files are now included in the result archive "output.tar.gz" so that it is the only file to download under one jobid.
-
-	This release also provides a python script, run_rapt.py, to run RAPT agnostically on customer's own system with python and docker-compatible container system installed. Refer to the documentation for details.
+This release updates PGAP to 2022-02-10.build5872