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Changed CLANS conda environment file (clans_2_1.yml) to use only the conda-forge channel without specific package versions.
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inbalpaz committed Nov 14, 2024
1 parent 503a538 commit 0c890ea
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44 changes: 17 additions & 27 deletions README.md
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# CLANS

CLANS 2.0 is a Python-based program for clustering sequences in the 2D or 3D space, based on their sequence similarities. CLANS visualizes the dynamic clustering process and enables the user to interactively control it and explore the cluster map in various ways.
CLANS 2.1 is a Python-based program for clustering sequences in the 2D or 3D space, based on their sequence
similarities. CLANS visualizes the dynamic clustering process and enables the user to interactively control it and
explore the cluster map in various ways.

## Overview

Expand All @@ -20,39 +22,23 @@ The BLAST search is only available in the command-line mode and requires Blast+

## Installation

**Requirements:** Anaconda installed on the target computer. An OS-specific version of Anaconda can be downloaded from: https://www.anaconda.com/.

### From Anaconda repository:

1. Create a clean conda environment: `conda create -n clans_2_0`

2. Activate the newly created environment: `conda activate clans_2_0`

3. Install the clans package from Anaconda repository by using the following command:

**On MacOS / Windows:**

`conda install -c inbalpaz clans -c defaults -c conda-forge`

**On Linux:**

`conda install -c inbalpaz clans_linux -c defaults -c conda-forge`

4. **On Linux only** run the following command: `pip install PyQt5`
**Requirements:** Anaconda or Miniconda installed on the target computer. An OS-specific version can be downloaded
from: https://www.anaconda.com/.

### From source using conda:

1. Download CLANS latest release from: https://github.com/inbalpaz/CLANS/releases.

2. Extract the tar.gz file into the desired working-directory.

3. Create a new conda environment using the ‘clans_2_0.yml’ file (located in the root directory of CLANS) using the following command:
3. Create a new conda environment using the ‘clans_2_1.yml’ file (located in the root directory of CLANS) using the
following command:

**On MacOS / Windows:** `conda env create -f clans_2_0.yml`
**On MacOS / Windows:** `conda env create -f clans_2_1.yml`

**On Linux:** `conda env create -f clans_2_0_linux.yml`
**On Linux:** `conda env create -f clans_2_1_linux.yml`

4. Activate the newly created environment: `conda activate clans_2_0`
4. Activate the newly created environment: `conda activate clans_2_1`

#### Set the display server on Linux
In case the default display server on your Linux distribution is Wayland, you should switch to Xorg (x11) in order to enable CLANS to work properly.
Expand All @@ -65,7 +51,7 @@ In case the default display server on your Linux distribution is Wayland, you sh

### Open the GUI-based visualisation tool

Within the activated clans_2_0 conda environment, type:
Within the activated clans_2_1 conda environment, type:

`python -m clans [-load <network file path>] [options]
`
Expand All @@ -74,9 +60,13 @@ When clans is executed without an input-file, the GUI is opened empty and an inp

### Running CLANS in command-line mode

The command-line mode is executed using the ‘-nogui’ flag option. It can be used to perform a BLAST search in order to create a matrix of sequence similarities and/or to perform a specific number of iterations of the force-directed graph layout calculation (which can be later loaded and displayed in the visualizing tool). It is also recommended in cases of large datasets, where the clustering can be done in the background and the resulted clans map can later be loaded and explored using the graphical interface.
The command-line mode is executed using the ‘-nogui’ flag option. It can be used to perform a BLAST search in order to
create a matrix of sequence similarities and/or to perform a specific number of iterations of the force-directed graph
layout calculation (which can be later loaded and displayed in the visualizing tool). It is also recommended in cases of
large datasets, where the clustering can be done in the background and the resulted clans map can later be loaded and
explored using the graphical interface.

Within the activated clans_2_0 conda environment, type:
Within the activated clans_2_1 conda environment, type:

`python -m clans -nogui -infile <fasta_file_path> -saveto <destination_file_path> [options]
`
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12 changes: 0 additions & 12 deletions clans_2_0.yml

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14 changes: 0 additions & 14 deletions clans_2_0_linux.yml

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11 changes: 11 additions & 0 deletions clans_2_1.yml
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name: clans_2_1
channels:
- conda-forge
dependencies:
- python
- numpy
- numba
- vispy
- pyqt
- biopython
- pillow
13 changes: 13 additions & 0 deletions clans_2_1_linux.yml
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name: clans_2_1
channels:
- conda-forge
dependencies:
- python
- numpy
- numba
- vispy
- biopython
- pillow
- pip
- pip:
- PyQt5
12 changes: 6 additions & 6 deletions conda_build/meta.yaml
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{% set name = "clans" %}
{% set version = "2.0.7" %}
{ % set version = "2.1.0" % }

package:
name: {{ name|lower }}
Expand All @@ -22,12 +22,12 @@ requirements:
- pip
run:
- python >=3.6
- numpy =1.20.3
- numba =0.53.1
- vispy =0.8.1
- pyqt =5.9.2
- numpy
- numba
- vispy
- pyqt
- biopython >=1.77
- pillow =8.3.1
- pillow

test:
imports:
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10 changes: 5 additions & 5 deletions conda_build_linux/meta.yaml
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@@ -1,5 +1,5 @@
{% set name = "clans_linux" %}
{% set version = "2.0.7" %}
{ % set version = "2.1.0" % }

package:
name: {{ name|lower }}
Expand All @@ -22,11 +22,11 @@ requirements:
- pip
run:
- python >=3.6
- numpy =1.20.3
- numba =0.53.1
- vispy =0.8.1
- numpy
- numba
- vispy
- biopython >=1.77
- pillow =8.3.1
- pillow

test:
imports:
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -2,7 +2,7 @@

setup(
name='clans',
version='2.0.2',
version='2.1.0',
packages=find_packages(),
package_data={'clans': [
'clans/clans/taxonomy/names.dmp',
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