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).