diff --git a/home.md b/home.md index 2af8a8d..a23f62a 100644 --- a/home.md +++ b/home.md @@ -27,11 +27,10 @@ Main features: Links: -* Official mirrors: - and . +* Official mirror: . * Source code at GitHub: . * Bioconductor package: . -* Docker image: . +* Docker image: . Citation: -* Zenkova D, Kamenev V, Sablina R, Artyomov M, Sergushichev A (2018). Phantasus: visual and interactive gene expression analysis. doi: 10.18129/B9.bioc.phantasus, . +* Kleverov M, Zenkova D, Kamenev V, Sablina R, Artyomov M, Sergushichev A (2022). Phantasus: web-application for visual and interactive gene expression analysis. doi:10.1101/2022.12.10.519861, https://www.biorxiv.org/content/10.1101/2022.12.10.519861. diff --git a/installation.md b/installation.md index 0965ed8..9fd420a 100644 --- a/installation.md +++ b/installation.md @@ -25,7 +25,7 @@ if (!requireNamespace("BiocManager", quietly = TRUE)) BiocManager::install("phantasus") ``` -However, the current set up instruction assumes **Phantasus version at least 1.23.4**, +However, the current set up instruction assumes **Phantasus version at least 1.23.5**, which can be installed from Bioconductor-devel (requires R version 4.4). Alternatively, the latest version of Phantasus can be installed from GitHub using `devtools` package. @@ -34,7 +34,7 @@ devtools::install_github("ctlab/phantasus") ``` -### System dependencies +### Dependencies There are several system packages that have to be installed on the system. The names of these packages will be displayed during installation. On Ubuntu one can @@ -44,6 +44,12 @@ install them beforehand and all together using command: sudo apt-get install libapparmor-dev libfontconfig1-dev libcairo2-dev libcurl4-openssl-dev pandoc libtiff5-dev libfribidi-dev libharfbuzz-dev libssl-dev libxml2-dev libprotobuf-dev protobuf-compiler ``` +Further, the latest version of `phantasus` depends on `rhdf5client (>= 1.25.1)` from Bioconductor 3.19, which on older systems can be more convenient to install from GitHub: + +```r +devtools::install_github("vjcitn/rhdf5client") +``` + ### Configuration Before the first run of Phantasus you need to setup it first. To perform interactive setup run: @@ -66,15 +72,15 @@ The configuration file includes the following parameters: | `cache_folders` | `geo_path: !expr file.path(cache_root, 'geo/')` | Folder with GEO-related cache files | | ^^ | {: style=";border-left: 1px solid #eeebee !important" } `annot_db: !expr file.path(cache_root, 'annotationdb/')` | Folder with gene annotation databases in sqlite format | | ^^ | {: style=";border-left: 1px solid #eeebee !important" } `fgsea_pathways:!expr file.path(cache_root, 'fgsea_pathways')` | Folder with pathways for `fgsea` package | -| ^^ | {: style=";border-left: 1px solid #eeebee !important" } `rnaseq_counts: "https://ctlab.itmo.ru/hsds/?domain=/counts"` | Folder with RNA-seq hdf5 files in ARCHs4-like format or URL to HSDS server| +| ^^ | {: style=";border-left: 1px solid #eeebee !important" } `rnaseq_counts: "https://alserglab.wustl.edu/hsds/?domain=/counts"` | Folder with RNA-seq hdf5 files in ARCHs4-like format or URL to HSDS server| | `geo_mirrors` | {: style=";border-left: 1px solid #eeebee !important" } `true_geo: "https://ftp.ncbi.nlm.nih.gov"` | GEO ftp server providing all files for related datasets | -| ^^ | {: style=";border-left: 1px solid #eeebee !important" } `minimal_cache: "https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/"` | Additional ftp server with a bunch of platform annotation files in machine readable format | +| ^^ | {: style=";border-left: 1px solid #eeebee !important" } `minimal_cache: "https://alserglab.wustl.edu/files/phantasus/minimal-cache/"` | Additional ftp server with a bunch of platform annotation files in machine readable format | The user which runs Phantasus has to have read and write permissions for all local paths mentioned in `user.conf`. -If some folder does not exist, the setup function will create it and will prompt you to fill it using the Phantasus [minimal cache mirror](https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/). +If some folder does not exist, the setup function will create it and will prompt you to fill it using the Phantasus [minimal cache mirror](https://alserglab.wustl.edu/files/phantasus/minimal-cache/). Setup function is able to load automatically files for `annot_db` and `fgsea_pathways` folders. -Files with RNA-seq count matrices, which are used in original Phantasus, are available at [minimal cache mirror](https://ctlab.itmo.ru/files/software/phantasus/minimal-cache/) too, but should be loaded manually if desired. However, we suggest the use of HSDS server by default which is able to load count matrices for RNA-seq datasets without storing any huge files. +Files with RNA-seq count matrices, which are used in original Phantasus, are available at [minimal cache mirror](https://alserglab.wustl.edu/files/phantasus/minimal-cache/) too, but should be loaded manually if desired. However, we suggest the use of HSDS server by default which is able to load count matrices for RNA-seq datasets without storing any huge files. ### Running @@ -95,11 +101,11 @@ You can customize serving of the application by specifying following parameters: ## Using Docker -To simplify deployment a phantasus docker image can be used. It is build regularly and is available at https://hub.docker.com/r/asergushichev/phantasus You can load the image with the following +To simplify deployment a phantasus docker image can be used. It is build regularly and is available at https://hub.docker.com/r/alserglab/phantasus You can load the image with the following command (assuming you have Docker installed and have permissions to use it): ```bash -docker pull asergushichev/phantasus +docker pull alserglab/phantasus ``` The dockerized Phantasus automatically configures itself on the @@ -115,7 +121,7 @@ mkdir phantasus-cache docker run -t -p 8000:8000 \ --env OCPU_USER=$UID \ --mount type=bind,source=`pwd`/phantasus-cache,target=/var/phantasus/cache \ - asergushichev/phantasus + alserglab/phantasus ``` After all resources are downloaded you will get the message, that Phantasus application is up and it becomes available at . The cached resources will be stored @@ -220,8 +226,8 @@ open by specifying the name in the URL: or -its mirror + where the latest versions are deployed. -Alternatively, Phantaus can be installed locally (see [Installation](installation.html)). +Alternatively, Phantasus can be installed locally (see [Installation](installation.html)). When Phantasus opens the starting screen should appear: diff --git a/tutorials/preparing.md b/tutorials/preparing.md index 87ef436..9b43c00 100644 --- a/tutorials/preparing.md +++ b/tutorials/preparing.md @@ -61,8 +61,7 @@ simultaneously. ## Basic controls -Now let us open the dataset in Phantasus. Use either - or +Now let us open the dataset in Phantasus. Use mirror. Then click on *Choose a file* input, select *GEO Datasets*, enter GSE53986 and click *Load* button (or press *Enter* on the keyboard).