From 73460e0574f9a153dba742cb151a5b34b10da110 Mon Sep 17 00:00:00 2001 From: Tanubrata Dey Date: Wed, 15 Nov 2023 13:40:57 -0500 Subject: [PATCH 1/2] Update: Updates Docker image w/ latest stable version in README --- README.md | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index fb7abc8..a0d9c1d 100755 --- a/README.md +++ b/README.md @@ -33,7 +33,24 @@ If you use JaBbA in your work, please cite: [Distinct Classes of Complex Structu ### Dockerized installation -A Docker container with the latest stable release of JaBbA and its dependencies installed can be found [here](https://hub.docker.com/r/graskind1/jabba) - many thanks to [grasskind](https://github.com/grasskind). +A Docker container with the latest stable release of JaBbA v1.1 and its dependencies installed can be found [here](https://hub.docker.com/r/mskilab/jabba). + +#### :warning: **Warning:** +> JaBbA depends on CPLEX MIP Optimizer to work. Because CPLEX is a proprietary software, it isn't included in the image and needs to be installed by the user. +> To add CPLEX: +> 1. Download CPLEX (Linux x86-64). (You may need to use the HTTP method.) +> 2. Pull image and run the container using: +> ``` +> docker pull mskilab/jabba:latest +> docker run -it --rm --platform linux/amd64 mskilab/jabba:latest +> ``` +> 3. Copy CPLEX binary into the container: docker cp /PATH/TO/DOWNLOADED_CPLEX.bin CONTAINER_ID:/opt/cplex_studio +> 4. Install CPLEX: /opt/cplex_studio/DOWNLOADED_CPLEX.bin (If you get a Permission denied error, run +> chmod 777 /PATH/TO/DOWNLOADED_CPLEX.bin before copying it into the container.) +> 5. When prompted for an installation path, type /opt/cplex. This is what the CPLEX_DIR environmental variable is set to. +> 6. Save changes to a new image for future use: +> Exit container (type exit or press Ctrl-D) +> Run docker commit CONTAINER_ID NEW_IMAGE_ID ### Installation from GitHub @@ -54,7 +71,7 @@ export CPLEX_DIR=/path/to/your/copy/of/CPLEX_Studio/ 3. Install JaBbA ```{r} -devtools::install_github('mskilab/JaBbA') +devtools::install_github('mskilab-org/JaBbA') ``` 4. For convenience, add `jba` executable to your `PATH` @@ -70,7 +87,7 @@ $ jba ## to see usage $ jba ${JABBA_PATH}/junctions.vcf ${JABBA_PATH}/coverage.txt ``` -**_WARNING_** : +:warning: **_WARNING_** : `JaBbA` uses some functions from `gGnome` package as a wrapper that needs`CPLEX` functionality to be added to `gGnome`. If the dependency package `gGnome` was installed before installing `JaBbA` or if CPLEX functionality was not added while installing `gGnome` or if you get an error while running JaBbA as shown below: ```{bash} Error in names(x) <- c("xopt", "obj", "status", "extra", "epgap") : @@ -92,7 +109,7 @@ As of ```v1.1``` JaBbA can now be run with [Gurobi](https://www.gurobi.com/produ 4. Install JaBbA ```{r} -devtools::install_github('mskilab/JaBbA') +devtools::install_github('mskilab-org/JaBbA') ``` 5. For convenience, add `jba` executable to your `PATH` From 92682b8c073153dd43e5245f24bc2173579e9a1b Mon Sep 17 00:00:00 2001 From: Tanubrata Dey Date: Wed, 15 Nov 2023 13:40:57 -0500 Subject: [PATCH 2/2] Update: Updates Docker image w/ latest stable version in README --- README.md | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index fb7abc8..e8af2a6 100755 --- a/README.md +++ b/README.md @@ -33,7 +33,25 @@ If you use JaBbA in your work, please cite: [Distinct Classes of Complex Structu ### Dockerized installation -A Docker container with the latest stable release of JaBbA and its dependencies installed can be found [here](https://hub.docker.com/r/graskind1/jabba) - many thanks to [grasskind](https://github.com/grasskind). +A Docker container with the latest stable release of JaBbA v1.1 and its dependencies installed can be found [here](https://hub.docker.com/r/mskilab/jabba). + +#### :warning: **Warning:** + +JaBbA depends on CPLEX MIP Optimizer to work. Because CPLEX is a proprietary software, it isn't included in the image and needs to be installed by the user. +To add CPLEX: +> 1. Download CPLEX (Linux x86-64). (You may need to use the HTTP method.) +> 2. Pull image and run the container using: +> ``` +> docker pull mskilab/jabba:latest +> docker run -it --rm --platform linux/amd64 mskilab/jabba:latest +> ``` +> 3. Copy CPLEX binary into the container: docker cp /PATH/TO/DOWNLOADED_CPLEX.bin CONTAINER_ID:/opt/cplex_studio +> 4. Install CPLEX: /opt/cplex_studio/DOWNLOADED_CPLEX.bin (If you get a Permission denied error, run +> chmod 777 /PATH/TO/DOWNLOADED_CPLEX.bin before copying it into the container.) +> 5. When prompted for an installation path, type /opt/cplex. This is what the CPLEX_DIR environmental variable is set to. +> 6. Save changes to a new image for future use: +> Exit container (type exit or press Ctrl-D) +> Run docker commit CONTAINER_ID NEW_IMAGE_ID ### Installation from GitHub @@ -54,7 +72,7 @@ export CPLEX_DIR=/path/to/your/copy/of/CPLEX_Studio/ 3. Install JaBbA ```{r} -devtools::install_github('mskilab/JaBbA') +devtools::install_github('mskilab-org/JaBbA') ``` 4. For convenience, add `jba` executable to your `PATH` @@ -70,7 +88,7 @@ $ jba ## to see usage $ jba ${JABBA_PATH}/junctions.vcf ${JABBA_PATH}/coverage.txt ``` -**_WARNING_** : +:warning: **_WARNING_** : `JaBbA` uses some functions from `gGnome` package as a wrapper that needs`CPLEX` functionality to be added to `gGnome`. If the dependency package `gGnome` was installed before installing `JaBbA` or if CPLEX functionality was not added while installing `gGnome` or if you get an error while running JaBbA as shown below: ```{bash} Error in names(x) <- c("xopt", "obj", "status", "extra", "epgap") : @@ -92,7 +110,7 @@ As of ```v1.1``` JaBbA can now be run with [Gurobi](https://www.gurobi.com/produ 4. Install JaBbA ```{r} -devtools::install_github('mskilab/JaBbA') +devtools::install_github('mskilab-org/JaBbA') ``` 5. For convenience, add `jba` executable to your `PATH`