Download the AnnoLnc2 standalone basic package(Version 2.1).
You can also find all source code and data at our ftp server, for more detailed information please see the section "Installation Guid" below.
Legacy:(We strongly suggest the lastest version of AnnoLnc, but if you are interested in the older version, you can find them here)
The AnnoLnc2 standalone package requires a computer with a modern Linux operating system, with a minimal requirement of 4 CPU cores, 8GB memory, 1.8TB free disk space for human and 1.1TB for mouse.
1. Download the standalone version package and uncompress the standalone package by run:
tar -zxvf AnnoLnc_2.1.tar.gz2. Build the AnnoLnc2 enviroment via conda
cd AnnoLnc_2.1
conda env create -f AnnoLnc2.yaml
conda activate AnnoLnc23. The upper instruction is used to install the source code and depency enviroment and third-party tools. For running basic annotation function, you should also download the basic data package and place it at the same directory as AnnoLnc_2.1.tar.gz, then uncompress it by run:
tar -zxvf AnnoLnc_2.1_basic_data.tar.gz
Notes:
1. Now AnnoLnc(version 2.1) support the test function. By simply run bash annolnc.sh -t hg38 or bash annolnc.sh -t mm10, you will find the result at the directory "human_test_out"(mouse_test_out). This function is used to check the whether the installion is successful and as a demo to show how AnnoLnc2 is worked and what's the results.
2.After finished the installion of AnnoLnc2 and downloaded the basic data package, users can run the follow modules: Genomic Location(include repeat elements), Secondary Structure(only support plot with entropy), Protein Interaction, Genetic Association, Subcellular Localization, Expression and co-Expression Function(for know lncRNA).
However, some backend data is too large, and only some modules require these files. More details are listed at the below table. If you would like to run the related modules, you should download them and place it at the same directory as AnnoLnc_2.1.tar.gz, then uncompress it by run: tar -zxvf XXX.tar.gz
| modules name | species | file download | size |
| transcription_regulation | hg38 | human_transcription_regulation.tar.gz | 4.8G |
| mm10 | mouse_transcription_regulation.tar.gz | 4.6G | |
| evolution | hg38 | human_evolution.tar.gz | 9.2G |
| mm10 | mouse_evolution.tar.gz | 8.2G | |
| miRNA_interaction | hg38 | human_miRNA_interaction.tar.gz | 97G |
| mm10 | mouse_miRNA_interaction.tar.gz | 33G | |
| expression and co_expression_function(for novel lncRNA) | hg38 | human_expression.tar.gz | 878G |
| mm10 | mouse_expression.tar.gz | 773G |
3. Conda is an open source package management system and environment management system. Support copy about thirty softwares which AnnoLnc2 needed to your local environment with the yaml file. If you don't like conda, you can install the thirty softwares by hand, refer to here.
User can run the Annolnc standalone version by simply run the following command:
bash annolnc.sh -i test/human_test.fa -o output -s hg38 -m /all Where -i specifies the input lncRNA fasta file to annotate, -o specifies the output directory to put annotations , -s specifies the genome build of species, and -m specifies the annotation modules to run.
Also, users can run bash annolnc.sh -h to view the complete help information.
AnnoLnc2 Develper Kit will provide user with all the data analysis pipelines in different annotation modules and the document to help users customize AnnoLnc2 with their own data rather than our backend data in TB size.
Here is the command used to build AnnoLnc2 conda enviroment. Most version of the softwares are compatible, except RNAfold(2.4.14), Stringtie(2), bedtools(>2.26), bx-python(0.7.3) and samtools(>1.7).
conda install -c conda-forge biopython #biopython-1.76
conda install -c anaconda pandas #pandas-0.24.2
conda install -c bioconda htslib #tabix=1.10.2
conda install -c bioconda r-stringr #r-stringr-1.4.0
conda install -c bioconda bioconductor-gostats #gostats-2.52.0
conda install -c bioconda r-snowfall #r-snowfall-1.84
conda install -c bioconda bx-python=0.7.3 #bx-python-0.7.3 better the same
conda install -c bioconda bedtools #bedtools-2.29.2 must bigger than or equal to 2.26
conda install -c anaconda mako #mako-1.1.1
conda install -c anaconda paste #paste-3.2.2
conda install -c anaconda sqlalchemy #sqlalchemy-1.3.9
conda install -c anaconda routes #routes-2.4.1
conda install -c anaconda webob #webob-1.8.5
conda install -c anaconda mercurial #mercurial-4.8.2
conda install -c anaconda pyyaml #pyyaml-5.1.2
conda install -c anaconda bz2file #bz2file-0.98
conda install -c anaconda webhelpers #webhelpers-1.3
conda install -c anaconda kombu #kombu-4.6.3
conda install -c anaconda h5py #h5py-2.9.0
conda install -c anaconda pysam #pysam-0.6
conda install -c anaconda cheetah #cheetah-2.4.4
conda install -c anaconda pycrypto
conda install -c r r-plyr #r-plyr-1.8.4
conda install -c bioconda viennarna #viennarna-2.4.14(RNAfold) must be the same
conda install -c bioconda stringtie=2.0 #stringtie-2.0 must be the same
conda install -c bioconda samtools=1.7
conda install -c bioconda cufflinks=2.2.1
conda install -c bioconda seqlogo=1.52
conda install -c r r-data.table