Merge pull request #9 from Puriney/master

🐶 📖 fix broken links on README

README.md

@@ -60,9 +60,9 @@ new-configuration-file -o /path/to/wonderful_CEL-Seq2_config.yaml
 
 Example of configuration is [here](https://github.com/yanailab/celseq2/blob/master/example/config.yaml).
 
-Example of CEL-Seq2 cell barcodes sequence dictionary is [here](https://gitlab.com/yanailab/celseq2/blob/master/example/barcodes_cel-seq_umis96.tab).
+Example of CEL-Seq2 cell barcodes sequence dictionary is [here](https://github.com/yanailab/celseq2/blob/master/example/barcodes_cel-seq_umis96.tab).
 
-Read ["Setup Configuration"](https://puriney.github.io/celseq2/user_guide/setup_config/)
+Read ["Setup Configuration"](https://yanailab.github.io/celseq2/user_guide/setup_config/)
 for full instructions.
 
 ### Step-2: Define Experiment Table
@@ -85,7 +85,7 @@ The content of experiment table in this example could be:
 | wonderful_experiment1     | 1-9              | path/to/lane2-R1.fastq.gz   | path/to/lane2-R2.fastq.gz   |
 | wonderful_experiment2     | 10-18                 | path/to/lane2-R1.fastq.gz | path/to/lane2-R2.fastq.gz   |
 
-Read ["Experiment Table Specification"](https://puriney.github.io/celseq2/user_guide/experiment_table/)
+Read ["Experiment Table Specification"](https://yanailab.github.io/celseq2/user_guide/experiment_table/)
 for full instructions when more complexed experiment designs take place.
 
 ### Step-3: Run Pipeline of `celseq2`
@@ -99,7 +99,7 @@ celseq2 --config-file /path/to/wonderful_CEL-Seq2_config.yaml \
     -j 10
 ```
 
-Read ["Launch Pipeline"](https://puriney.github.io/celseq2/user_guide/launch_pipeline/)
+Read ["Launch Pipeline"](https://yanailab.github.io/celseq2/user_guide/launch_pipeline/)
 for full instructions to see how to submit jobs to cluster, or preview how many
 tasks are going to be scheduled.
 

celseq2/demultiplex.py

@@ -41,7 +41,7 @@ def bc_dict_seq2id(bc_index_fpath, col_seq=None):
             if row.startswith('#'):
                 continue
             row = row.strip().split()
-            print('{}:{}'.format(row_num, row))
+            # print('{}:{}'.format(row_num, row))
             row_val = row[col_seq]
             row_key = row_num
             out[row_key] = row_val
@@ -63,7 +63,7 @@ def bc_dict_id2seq(bc_index_fpath, col_seq=None):
             if row.startswith('#'):
                 continue
             row = row.strip().split()
-            print('{}:{}'.format(row_num, row))
+            # print('{}:{}'.format(row_num, row))
             row_val = row[col_seq]
             row_key = row_num
             out[row_key] = row_val

celseq2/version.py

-__version__ = '0.4.3'
+__version__ = '0.4.4'

celseq2/workflow/celseq2.snakemake

@@ -122,6 +122,14 @@ rule Count_Matrix:
         touch('_done_UMI')
     message: 'Finished counting UMI-count matrix.'
     run:
+        if ALIGNER == 'star':
+            shell('rm {}'.format('_done_star_genome_loaded'))
+            print('Free memory loaded by STAR', flush=True)
+            cmd  = 'STAR '
+            cmd += '--genomeLoad Remove '
+            cmd += '--genomeDir {STAR_INDEX_DIR} '
+            shell(cmd)
+
         print_logger('UMI-count matrix is saved at {}'.format(input.csv))
 
 
@@ -162,17 +170,17 @@ rule celseq2:
     run:
         if glob.glob('celseq2_job*.sh*'):
             shell('mv -f celseq2_job*.sh* {}'.format(SUBDIR_QSUB))
-
-        print_logger('Expression UMI matrix is saved at {}'.format(input.csv))
-
         if ALIGNER == 'star':
-            shell('rm {}'.format(rules.star_load_genome.output))
+            shell('rm {}'.format('_done_star_genome_loaded'))
             print('Free memory loaded by STAR', flush=True)
             cmd  = 'STAR '
             cmd += '--genomeLoad Remove '
             cmd += '--genomeDir {STAR_INDEX_DIR} '
             shell(cmd)
 
+        print_logger('Expression UMI matrix is saved at {}'.format(input.csv))
+
+
 rule setup_dir:
     input: SAMPLE_TABLE_FPATH
     output:

docs/about/release_note.md

@@ -10,14 +10,14 @@
 
 ---
 
-## :fa-flag-checkered: **v0.4.3**
+## :fa-flag-checkered: **v0.4.4**
 
 :fa-calendar: **2018-02-13**
 
 :fa-star: **Features**
 
-- Improve the design of snakemake pipeline to avoid silent pre-inhibition.
-- Better support STAR to avoid memory overuse.
+- Improve the design of `snakemake` pipeline to avoid silent pre-inhibition.
+- Improve running with STAR to avoid memory over-use.
 
 ---
 

setup.py

@@ -112,6 +112,7 @@ setup(
             # 'sphinx-argparse',
             # 'mock',
             'mkdocs',
+            'mkdocs-material',
             'fontawesome_markdown',
             'mkdocs-bootswatch',
             'pymdown-extensions',