diff --git a/README.md b/README.md index df2d832..bd91e29 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ docker pull mingxuangao/dreamdia:v1.0.0 docker run -it --name dreamdia_example --gpus all -v /YOUR/OWN/WORK/PATH:/tmp/work mingxuangao/dreamdia:v1.0.0 /bin/bash ``` -* Using the argument `--gpus all` will considerably accelerate the Dream-DIA-XMBD pipeline if you have some GPUs. +* Using the argument `--gpus all` will considerably accelerate the DreamDIA-XMBD pipeline if you have some GPUs. 3. Activate the conda environment. @@ -58,8 +58,8 @@ If .raw files are going to be fed directly to Dream-DIA-XMBD in Linux systems, [ ### Installation ```bash -git clone https://github.com/xmuyulab/Dream-DIA-XMBD -cd Dream-DIA-XMBD +git clone https://github.com/xmuyulab/DreamDIA-XMBD +cd DreamDIA-XMBD bash build.sh ``` @@ -79,7 +79,7 @@ python Dream-DIA/DreamDIA.py dreamscore --file_dir rawdata_dir --lib library.tsv * Centroided .mzML or .mzXML files are supported at any time. -* If .raw files are going to be fed directly to Dream-DIA-XMBD in Linux systems, [mono](https://www.mono-project.com/download/stable/#download-lin) must be installed first for the data format conversion by ThermoRawFileParser. +* If .raw files are going to be fed directly to DreamDIA-XMBD in Linux systems, [mono](https://www.mono-project.com/download/stable/#download-lin) must be installed first for the data format conversion by ThermoRawFileParser. * You can also use our docker image to process .raw files directly, while it may take some time for data format conversion. @@ -99,11 +99,11 @@ All raw data files should be at the same directory as below. #### 2. Spectral libraries -Only .tsv libraries are supported. All of the fields required by Dream-DIA-XMBD are listed in `Dream-DIA/lib_col_settings`. Users can modify this file to adjust their own spectral libraries. +Only .tsv libraries are supported. All of the fields required by DreamDIA-XMBD are listed in `Dream-DIA/lib_col_settings`. Users can modify this file to adjust their own spectral libraries. #### 3. window setting file -Dream-DIA-XMBD needs a tab separated window setting file **without overlapping** among the isolation windows as OpenSWATH. An example window setting file for classical SWATH acquisition strategy is shown below. +DreamDIA-XMBD needs a tab separated window setting file **without overlapping** among the isolation windows as OpenSWATH. An example window setting file for classical SWATH acquisition strategy is shown below. ``` 399 424.5 @@ -142,4 +142,4 @@ Dream-DIA-XMBD needs a tab separated window setting file **without overlapping** #### 4. output -Dream-DIA-XMBD outputs peptide and protein identification and quantification results. An empty directory is suggested for the `--out` argument to save all of the output files. +DreamDIA-XMBD outputs peptide and protein identification and quantification results. An empty directory is suggested for the `--out` argument to save all of the output files.