From bb9c8b9bc7c391c4a78d5ac8e7817fea9654a547 Mon Sep 17 00:00:00 2001 From: RAPT-release Date: Wed, 5 Jan 2022 14:59:55 -0500 Subject: [PATCH] RAPT v0.5.0 - teamcity CI --- GCP RAPT.md | 2 +- README.md | 2 +- Standalone RAPT.md | 2 +- dist/CHANGELOG.md | 5 +++++ dist/README.txt | 2 +- dist/release-notes.txt | 11 ++++++----- dist/run_rapt.py | 4 ++-- dist/run_rapt_gcp.sh | 4 ++-- 8 files changed, 19 insertions(+), 13 deletions(-) diff --git a/GCP RAPT.md b/GCP RAPT.md index 8a7a8fa..2e53033 100644 --- a/GCP RAPT.md +++ b/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/v0.4.2/rapt-v0.4.2.tar.gz + ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.0/rapt-v0.5.0.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. diff --git a/README.md b/README.md index d4fe777..c789cca 100644 --- a/README.md +++ b/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/v0.4.2/rapt-v0.4.2.tar.gz +~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.0/rapt-v0.5.0.tar.gz ~$ tar -xzf rapt.tar.gz && rm -f rapt.tar.gz ``` diff --git a/Standalone RAPT.md b/Standalone RAPT.md index 7e4aea3..c7b7099 100644 --- a/Standalone RAPT.md +++ b/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:
``` - ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.4.2/rapt-v0.4.2.tar.gz + ~$ curl -sSLo rapt.tar.gz https://github.com/ncbi/rapt/releases/download/v0.5.0/rapt-v0.5.0.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
diff --git a/dist/CHANGELOG.md b/dist/CHANGELOG.md index d10d0ca..6e231a8 100644 --- a/dist/CHANGELOG.md +++ b/dist/CHANGELOG.md @@ -1,3 +1,8 @@ +### 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 diff --git a/dist/README.txt b/dist/README.txt index 7643071..707c57e 100644 --- a/dist/README.txt +++ b/dist/README.txt @@ -1,4 +1,4 @@ -Read Assembly and Annotation Pipeline Tool (RAPT) v0.4.2 +Read Assembly and Annotation Pipeline Tool (RAPT) v0.5.0 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 index a88b714..2440a9c 100644 --- a/dist/release-notes.txt +++ b/dist/release-notes.txt @@ -1,9 +1,10 @@ -RELEASE: v0.4.2 -DATE: 10-25-2021 -BUILD: rapt-35244699 +RELEASE: v0.5.0 +DATE: 01-05-2022 +BUILD: rapt-36255426 SKESA: 2.5.0 -PGAPX: 2021-07-01.build5508 +PGAPX: 2021-11-29.build5742 DESCRIPTION: -This release update SKESA to use a newer version of boost in order to handle some flavor of gzipped input file. \ No newline at end of file +This release updated PGAPX to 2021-11-29.build5742 and use dedicated program instead of curl to fetch SRA data. + diff --git a/dist/run_rapt.py b/dist/run_rapt.py index 1cb634b..6b316c0 100755 --- 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:v0.4.2" +IMAGE_URI="ncbi/rapt:v0.5.0" -RAPT_VERSION="rapt-35244699" +RAPT_VERSION="rapt-36255426" DEFAULT_REF_DIR = '.rapt_refdata' diff --git a/dist/run_rapt_gcp.sh b/dist/run_rapt_gcp.sh index 4ab1746..2e22cf4 100755 --- 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:v0.4.2" -RAPT_VERSION="rapt-35244699" +IMAGE_URI="ncbi/rapt:v0.5.0" +RAPT_VERSION="rapt-36255426" GCP_LOGS_VIEWER="https://console.cloud.google.com/logs/viewer"