RAPT v0.4.2 - 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/v0.4.1/rapt-v0.4.1.tar.gz
+    ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.4.2/rapt-v0.4.2.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

@@ -8,7 +8,7 @@ If you are new to RAPT, please visit our [wiki page](https://github.com/ncbi/rap
 
 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/v0.4.1/rapt-v0.4.1.tar.gz
+~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.4.2/rapt-v0.4.2.tar.gz
 ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz
 ```
 

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/v0.4.1/rapt-v0.4.1.tar.gz
+    ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.4.2/rapt-v0.4.2.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

@@ -1,3 +1,6 @@
+### 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

dist/README.txt

@@ -1,4 +1,4 @@
-Read Assembly and Annotation Pipeline Tool (RAPT) v0.4.1
+Read Assembly and Annotation Pipeline Tool (RAPT) v0.4.2
 
 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

@@ -1,9 +1,9 @@
-RELEASE: v0.4.1
-DATE: 10-12-2021
-BUILD: rapt-34986039
+RELEASE: v0.4.2
+DATE: 10-25-2021
+BUILD: rapt-35244699
 SKESA: 2.5.0
 PGAPX: 2021-07-01.build5508
 
 DESCRIPTION:
 
-This release fixed a bug (double quote of version string that causes syntax error when running standalone run_rapt.py), added logic to tolerate minor taxonomy name mismatch, and retry upon SRA download failure caused by network glitches.
+This release update SKESA to use a newer version of boost in order to handle some flavor of gzipped input file.

dist/run_rapt.py

@@ -12,9 +12,9 @@
 ##to be compatible with python2
 from abc import ABCMeta, abstractmethod
 
-IMAGE_URI="ncbi/rapt:v0.4.1"
+IMAGE_URI="ncbi/rapt:v0.4.2"
 
-RAPT_VERSION="rapt-34986039"
+RAPT_VERSION="rapt-35244699"
 
 DEFAULT_REF_DIR = '.rapt_refdata'
 

dist/run_rapt_gcp.sh

@@ -1,8 +1,8 @@
 #!/usr/bin/env bash
 
 ###############################* Global Constants *##################################
-IMAGE_URI="ncbi/rapt:v0.4.1"
-RAPT_VERSION="rapt-34986039"
+IMAGE_URI="ncbi/rapt:v0.4.2"
+RAPT_VERSION="rapt-35244699"
 
 GCP_LOGS_VIEWER="https://console.cloud.google.com/logs/viewer"