minor revised

zhangrengang · Oct 29, 2020 · 54f4bfd · 54f4bfd
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Showing 8 changed files with 18 additions and 7 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,10 @@
 .DS_Store
+TEsorter/database/*.hmm.h3*
+*/*.pyc
+*/__pycache__/
+*/*/__pycache__/
+.gitignore
+dist/
+build/
+TEsorter.egg-info/
+rice*
diff --git a/README.md b/README.md
@@ -29,23 +29,25 @@ conda install -c bioconda tesorter
 Dependencies:
 +    [python >3](https://www.python.org/)  
 	+   [biopython](https://biopython.org/): quickly install by `pip install biopython` or `conda install biopython`  
-	+   [parallel python v1.6.4.4](https://www.parallelpython.com/): quickly install by `conda install pp`
+	+   [parallel python v1.6.4.4](https://www.parallelpython.com/): quickly install by `conda install -c bioconda pp`
 +   [hmmscan 3.1x or 3.2x](http://hmmer.org/): be compatible with HMMER3/f database format. quickly install by `conda install hmmer`
 +   [blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download): quickly install by `conda install blast`
 + TEsorter:
 ```
-git clone https://github.com/NBISweden/TEsorter
+git clone https://github.com/zhangrengang/TEsorter
 cd TEsorter
 python setup.py install
 ```
 ## Quick Start
 ```
-# run
+# run the example
 TEsorter-test
+# or
+TEsorter TEsorter/test/rice6.9.5.liban
 ```
 By default, the newly released [REXdb](http://repeatexplorer.org/?page_id=918) ([viridiplantae_v3.0 + metazoa_v3](https://bitbucket.org/petrnovak/re_databases)) database is used, which is more sensitive and more common and thus is recommended.
 
-For plants, it might be better to use only the plant database:
+For plants ([an example](https://raw.githubusercontent.com/oushujun/EDTA/master/database/rice6.9.5.liban)), it might be better to use only the plant database:
 ```
 TEsorter input_file -db rexdb-plant
 ```

diff --git a/TEsorter/__init__.pyc b/TEsorter/__init__.pyc
diff --git a/TEsorter/__pycache__/__init__.cpython-39.pyc b/TEsorter/__pycache__/__init__.cpython-39.pyc
diff --git a/TEsorter/__pycache__/version.cpython-39.pyc b/TEsorter/__pycache__/version.cpython-39.pyc
diff --git a/TEsorter/version.py b/TEsorter/version.py
@@ -1 +1 @@
-__version__ = '1.2.6'
+__version__ = '1.3'
diff --git a/TEsorter/version.pyc b/TEsorter/version.pyc
diff --git a/setup.py b/setup.py
@@ -10,9 +10,9 @@
 setup(
     name='TEsorter',
     version=__version__,
-    description='Lineage-level classification of transposable elements using conserved protein domains',
+    description='TEsorter: clade-level classification of transposable elements reflecting phylogenies and diversities',
     url='https://github.com/zhangrengang/TEsorter',
-    download_url='https://github.com/zhangrengang/TEsorter/archive/v1.2.6.tar.gz',
+    download_url='https://github.com/zhangrengang/TEsorter/archive/v1.3.tar.gz',
     author='Zhang, Ren-Gang and Wang, Zhao-Xuan, Jacques Dainat',
     license='GPL-3.0',