ScSmOP Installation Checking - ZhengmzLab/ScSmOP GitHub Wiki

1. Successful installation

A successful installation check list:

1.1 Unzipped configuration files under ConfigFiles

    $ ls ConfigFiles
        10x_scarc-atac_config.json  10x_spatial-rna_config.json                OriginalConfigFile_rdSPRITE.json          chia-drop_config.json
        10x_scarc-rna_config.json   OriginalConfigFile.json                    OriginalConfigFile_scARC-scATAC-seq.json  dropseq_scrna_config.json
        10x_scatac_v2_config.json   OriginalConfigFile_ChIA-Drop.json          OriginalConfigFile_scARC-scRNA-seq.json   rdsprite_config.json
        10x_scrna_v2_config.json    OriginalConfigFile_SPRITE.json             OriginalConfigFile_scATAC-seq.json        scsprite_config.json
        10x_scrna_v3_config.json    OriginalConfigFile_Spatial-scRNA-seq.json  bgi_scrna-seq_config.json                 sprite_config.json

1.2 Unzipped barcode whitelist files under BarcodeBucket

    $ ls BarcodeBucket
        3M-february-2018.txt            SPRITE.EVEN.txt      rdSPRITE.ODD.txt             scSPRITE_Y_Barcode.txt     visium-v4.txt
        4M-with-alts-february-2016.txt  SPRITE.ODD.txt       rdSPRITE.RPM.txt             visium-v1.txt              visium-v4_coordinates.txt
        737K-arc-v1-scatac.txt          SPRITE.Y.txt         rdSPRITE.Y.txt               visium-v1_coordinates.txt  visium-v5.txt
        737K-arc-v1-scrna.txt           dpm96.fasta          scSPRITE_DPMPRE_Barcode.txt  visium-v2.txt              visium-v5_coordinates.txt
        737K-august-2016.txt            rdSPRITE.DPM.txt     scSPRITE_DPM_Barcode.txt     visium-v2_coordinates.txt
        737K-cratac-v1.txt              rdSPRITE.EVEN.txt    scSPRITE_EVEN_Barcode.txt    visium-v3.txt
        SPRITE.DPM.txt                  rdSPRITE.LIGTAG.txt  scSPRITE_ODD_Barcode.txt     visium-v3_coordinates.txt

1.3 Executable pipeline (-rwxrwxrwx) scripts files under PipelineScript

    $ ls -l PipelineScript/
        -rwxrwxrwx 1 kasenjing kasenjing  1117 Sep 25 23:37 10x_scrna-v2.sh
        -rwxrwxrwx 1 kasenjing kasenjing  7075 Sep 25 20:19 BarcodeIdentification.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1518 Sep 25 20:19 ChIA-Drop.sh
        -rwxrwxrwx 1 kasenjing kasenjing 16915 Oct 11 16:33 GroupAndDataRefine.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1438 Oct  9 19:54 HiC.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1423 Sep 25 20:19 Lanuch_ChIA-Drop.sh
        -rwxrwxrwx 1 kasenjing kasenjing 14937 Sep 25 20:19 QualityAssessment.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1784 Sep 25 20:19 SPRITE.sh
        -rwxrwxrwx 1 kasenjing kasenjing 10753 Oct 11 22:58 SequenceAlignment.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1119 Sep 25 23:37 dropseq_scrna.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1682 Sep 25 20:19 rdSPRITE.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1418 Sep 25 20:19 scATAC.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1140 Oct 23 18:13 scRNA.sh
        -rwxrwxrwx 1 kasenjing kasenjing  1293 Sep 25 20:19 scSPRITE.sh
        -rwxrwxrwx 1 kasenjing kasenjing  2858 Sep 25 23:37 scarc.sh

1.4 Executable bioinformatic tools under Tools

    $ ls Tools
        BARP    
        Rscript  
        STARM.tar.gz      
        bedtools  
        cutadapt                  
        macs2      
        pigz     
        samtools
        FastQC  
        STAR     
        TrimGalore-0.6.6  
        bwa       
        juicer_tools_1.19.01.jar  
        pairtools  
        python3  
        trim_galore

Some of these tools are used in processing all kinds of data while some of these don't (Detail).

2. Software & Version

Tool	Version	Used in	URL
BARP	0.0.1	All	This Repository
samtools	1.18	All	https://github.com/samtools/samtools
trim_galore	0.6.6	SPRITE, scSPRITE, RD-SPRITE	https://github.com/FelixKrueger/TrimGalore
cutadapt	4.5	SPRITE, scSPRITE, RD-SPRITE	https://github.com/marcelm/cutadapt/
STAR*	2.7.10	RNA data of All technologies	This Repository
bedtools	2.31.0	SPRITE, scARC-seq ATAC part, scATAC-seq	https://github.com/arq5x/bedtools2
macs2	2.2.9.1	scARC-seq ATAC part, scATAC-seq	https://github.com/macs3-project/MACS/wiki/Install-macs2
bwa	0.7.17	Technologies with DNA fragment	https://github.com/lh3/bwa
Rscript	4.3.1	ChIA-Drop, scARC-seq ATAC part, scATAC-seq	https://www.r-project.org/
pairtools	1.0.2	scAIR-seq	https://github.com/open2c/pairtools
pigz	2.4	scAIR-seq	https://github.com/madler/pigz

* Modified STAR source code to make it capable of processing BARP produced FASTQ files while retaining exact other functions.

3. Trouble Shooting of Installation

There are two kinds of reminders if some tools failed to install:

3.1 Tools installed with conda: samtools macs2 bedtools Rscript bwa pairtools

    Installation of [Tool] failed, you may need to reinstall them with

            conda install [Tool] -n ScSmOP -y

    or you can link one of your previously installed  to the directory of ScSmOP/Tools

Reinstall Tools, for example: macs2:

    conda install macs2=2.2.9.1 -n ScSmOP -y

3.2 Tools compiled locally: BARP STAR

    Installation of  failed, it may caused by the failed installation of "gcc", "g++", reinstall these with
            conda install -c conda-forge/label/cf202003 cxx-compiler -y -n ScSmOP
            conda install make -n ScSmOP -y -c conda-forge
    and then recompile it.

These tools need gcc and g++ to compile them.

After install gcc and g++, recompile BARP as follow (suppose you are under directory ScSmOP):

    cd BARP-prog
    make
    cd ..
    ln -s BARP-prog/BARP Tools/BARP

Recompile STAR as follow (suppose you are under directory ScSmOP):

    cd Tools
    tar -zxvf STARM.tar.gz
    cd STARM/source
    make STAR
    cd ../..
    mv STARM/source/STAR .
    rm -r STARM