Unverified Commit 8031a2bc authored by Yun YAN's avatar Yun YAN Committed by GitHub
Browse files

Merge pull request #9 from Puriney/master

🐶 📖 fix broken links on README
parents 040d2014 933ebcae
......@@ -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.
......
......@@ -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
......
__version__ = '0.4.3'
__version__ = '0.4.4'
......@@ -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:
......
......@@ -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.
---
......
......@@ -112,6 +112,7 @@ setup(
# 'sphinx-argparse',
# 'mock',
'mkdocs',
'mkdocs-material',
'fontawesome_markdown',
'mkdocs-bootswatch',
'pymdown-extensions',
......
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