RAPT v0.5.4 - teamcity CI

ncbi · Dec 7, 2022 · 1641bcf · 1641bcf
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diff --git a/README.md b/README.md
@@ -7,14 +7,15 @@ With RAPT you will:<br>
 * **assemble your reads** into contigs<br>
 * **assign a scientific name** to the assembly<br>
 * **predict coding and non-coding genes** *de novo*, including anti-microbial resistance (AMR) genes and virulence factors, based on expert-curated data such as hidden Markov models and conserved domain architectures<br>
+* **estimate the completeness and contamination level** of the annotated assembly<br>
 
 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_context_Apr2022.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/v0.5.3/rapt-v0.5.3.tar.gz
+~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.4/rapt-v0.5.4.tar.gz
 ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
 ```
 

diff --git a/dist/CHANGELOG.md b/dist/CHANGELOG.md
@@ -1,3 +1,7 @@
+### Release v0.5.4
+# Update PGAPX to 2022-10-03.build6384
+
+
 ### Release v0.5.3
 # Bugfix: SRA/metadata retrieval methods correction according to the recent change of corresponding services
 

diff --git a/dist/README.txt b/dist/README.txt
@@ -1,4 +1,4 @@
-Read Assembly and Annotation Pipeline Tool (RAPT) v0.5.3
+Read Assembly and Annotation Pipeline Tool (RAPT) v0.5.4
 
 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. 
 

diff --git a/dist/release-notes.txt b/dist/release-notes.txt
@@ -1,9 +1,10 @@
-RELEASE: v0.5.3
-DATE: 07-15-2022
-BUILD: rapt-39223259
+RELEASE: v0.5.4
+DATE: 12-07-2022
+BUILD: rapt-41589182
 SKESA: 2.5.0
-PGAPX: 2022-04-14.build6021
+PGAPX: 2022-10-03.build6384
 
 DESCRIPTION:
 
-This is a bugfix release. The methods to retrieve SRA and metadata have been modified to align with the recent change to the backend services
+Update PGAPX to 2022-10-03.build6384
+
diff --git a/dist/run_rapt.py b/dist/run_rapt.py
@@ -12,9 +12,9 @@
 ##to be compatible with python2
 from abc import ABCMeta, abstractmethod
 
-IMAGE_URI="ncbi/rapt:v0.5.3"
+IMAGE_URI="ncbi/rapt:v0.5.4"
 
-RAPT_VERSION="rapt-39223259"
+RAPT_VERSION="rapt-41589182"
 
 DEFAULT_REF_DIR = '.rapt_refdata'
 

diff --git a/dist/run_rapt_gcp.sh b/dist/run_rapt_gcp.sh
@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
 ###############################* Global Constants *##################################
-IMAGE_URI="ncbi/rapt:v0.5.3"
-RAPT_VERSION="rapt-39223259"
+IMAGE_URI="ncbi/rapt:v0.5.4"
+RAPT_VERSION="rapt-41589182"
 
 GCP_LOGS_VIEWER="https://console.cloud.google.com/logs/viewer"