diff --git a/CHANGELOG.md b/CHANGELOG.md index d571e45..a751d72 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,10 +1,25 @@ +# v1.2.0 +## Features +- Added an option to skip characterization/comparative analysis steps +- Enhanced the Docker shell script (asap-docker.sh) (more options, use user:group file ownerships) +- Replaced RDP 16S db by SILVA +- Added classification of all detected and valid 16S sequences in taxonomic classification +- Added a 'debug' option for better on-site/remote debugging + +## Enhancements +- Updated PubMLST to 2019-10-02 +- Updated CARD db to 3.0.5 and RGI to 5.1.0 +- Updated VFDB to 2019-10-02 +- Discarded unnecessary dependencies from Docker image +- Applied several bugfixes and minor improvements to report pages + # v1.1.3 ## Enhancements - Added a dynamic max cpu/core threshold for 3rd party executables (#2) - Fixed data table localization - Fixed scaffold table download file names - Removed unnecessary dependencies -- updated source code library versions +- Updated source code library versions # v1.1.2 ## Enhancements diff --git a/README.md b/README.md index bb8a696..ab8a56b 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@ analysed as a single project, we distribute ASA³P in two versions: For both the following files are necessary: - ASA³P tarball (asap.tar.gz) containing binaries, 3rd party executables and databases: -https://s3.computational.bio.uni-giessen.de/swift/v1/asap/asap.tar.gz +https://s3.computational.bio.uni-giessen.de/swift/v1/asap/asap.tar.gz (md5 sum: 2953627f543667d19166e77c86573e81) - configuration template: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/config.xls Note: @@ -74,9 +74,9 @@ Additional files: - comprehensive manual: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/manual.pdf - configuration example: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/config-example.xls - example projects: - - 4 public *L. monocytogenes* genomes: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/example-lmonocytogenes-4.tar.gz - - 32 public *L. monocytogenes* genomes: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/example-lmonocytogenes-32.tar.gz - - 8 *E. coli* project merely showing support of different input types: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/example-ecoli-input.tar.gz + - 4 public *L. monocytogenes* genomes: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/example-lmonocytogenes-4.tar.gz (md5sum: 3da5858e62a3c8a836dfa91e58a9983e) + - 32 public *L. monocytogenes* genomes: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/example-lmonocytogenes-32.tar.gz (md5sum: 4e64aa96f24dff518dead76f150a936c) + - 8 *E. coli* project merely showing support of different input types: https://s3.computational.bio.uni-giessen.de/swift/v1/asap/example-ecoli-input.tar.gz (md5sum: 1da85ab18f9afae98cf176ef88c6c214) ### Docker For small to medium projects (up to ~200 isolates) but also for the sake of @@ -144,7 +144,7 @@ information please have a look at our user manual. In order to trigger an **OpenStack** based cloud project, you need the following additional cloud related files: - ASA³P cloud tarball (containing binaries, property files and a customized BiBiGrid version): -https://s3.computational.bio.uni-giessen.de/swift/v1/asap/asap-cloud.tar.gz +https://s3.computational.bio.uni-giessen.de/swift/v1/asap/asap-cloud.tar.gz (md5sum: c584dedcaf17963a240dbabfad95f608) Once ASA³P is properly setup you can start it by executing a single shell script: ```bash diff --git a/core/pom.xml b/core/pom.xml index 79059f2..4b4c89a 100644 --- a/core/pom.xml +++ b/core/pom.xml @@ -5,7 +5,7 @@ bio.comp.jlu.asap asap - 1.1.3 + 1.2.0 jar ASAP diff --git a/core/src/main/java/bio/comp/jlu/asap/ASAPConstants.java b/core/src/main/java/bio/comp/jlu/asap/ASAPConstants.java index c960aac..d81ba37 100644 --- a/core/src/main/java/bio/comp/jlu/asap/ASAPConstants.java +++ b/core/src/main/java/bio/comp/jlu/asap/ASAPConstants.java @@ -12,6 +12,6 @@ public final class ASAPConstants { public final static int MAX_STEP_WAITING_PERIOD = 24*60*60*1000; public final static int EXP_BACKOFF_EXP = 10; -public final static String ASAP_VERSION = "1.1.3"; +public final static String ASAP_VERSION = "1.2.0"; -} +} \ No newline at end of file