Is it possible to get the Wine path to a file on the current OS?
Example:
wine-get-path ~/foo.txt # Outputs: Z:\\Users\Tyilo\foo.txt
wine-get-path ~/.wine/drive_c/windows/explorer.exe # Output: C:\\windows\\explorer.exe
where wine-get-path would be the function I need.
The answer is winepath -w foofile
Related
I have written a snakemake code to run bwa_map. Fastq files are with different folder name and different sample name (paired end). It shows error as 'SAMPLES' is not defined. Please help.
Error:
$snakemake --snakefile rnaseq.smk mapped_reads/EZ-123-B_IGO_08138_J_2_S101_R2_001.bam -np
*NameError in line 2 of /Users/singhh5/Desktop/tutorial/rnaseq.smk:
name 'SAMPLES' is not defined
File "/Users/singhh5/Desktop/tutorial/rnaseq.smk", line 2, in *
#SAMPLE DIRECTORY
fastq
Sample_EZ-123-B_IGO_08138_J_2
EZ-123-B_IGO_08138_J_2_S101_R1_001.fastq.gz
EZ-123-B_IGO_08138_J_2_S101_R2_001.fastq.gz
Sample_EZ-123-B_IGO_08138_J_4
EZ-124-B_IGO_08138_J_4_S29_R1_001.fastq.gz
EZ-124-B_IGO_08138_J_4_S29_R2_001.fastq.gz
#My Code
expand("~/Desktop/{sample}/{rep}.fastq.gz", sample=SAMPLES)
rule bwa_map:
input:
"data/genome.fa",
"fastq/{sample}/{rep}.fastq"
conda:
"env.yaml"
output:
"mapped_reads/{rep}.bam"
threads: 8
shell:
"bwa mem {input} | samtools view -Sb -> {output}"
The specific error you are seeing is because the variable SAMPLES isn't set to anything before you use it in expand.
Some other issues you may run into:
Output file is missing the {sample} wildcard.
The value of threads isn't passed into bwa or samtools
You should place your expand into the input directive of the first rule in your snakefile, typically called all to properly request the files from bwa_map.
You aren't pairing your reads (R1 and R2) in bwa.
You should look around stackoverflow or some github projects for similar rules to give you inspiration on how to do this mapping.
I implemented test cases for my application and decided to run it everyday. The problem is the result of the previous test will be overwritten by the latest test result. I need to keep them both so I came up with a solution that include the test date and time in the report name, for example; report-202111181704.html (use time in 24-hour format).
I searched through the internet and did not found any solution yet. Anybody here know the solution? or any alternative solution will be fine.
It depends on where you execute your tests. From command line you can save the date to variable. Then use this variable to change the name of generated outputs. For example
date=$(date '+%Y-%m-%d_%H:%M:%S')
robot --output ${date}output.xml --log ${date}log.html --report ${date}report.html test.robot
I found the solution. Instead of setting .html file name, I create a folder and put the result there.
To do this, add --outputdir in pabot command so it's gonna look like this
pabot --pabotlibport $PABOT_PORT --pabotlib --resourcefile ./DeviceSet.dat --processes $thread --verbose --outputdir ./result/$OUTPUT_DIR $ENV
where
$OUTPUT_DIR=`date + "%Y%m%d-%H%M"`
The output folder gonna be like ./result/20220301-2052
Not sure how I should be going about this, but it is not working currently:
My first thought: in my home directory, I have the folder for GC SDK:
Sys.setenv(PATH="$HOME/google-cloud-sdk")
system(paste0("gsutil cp ",paste0(bucket,cancer.id,"/rnaseq_fpkm_*.csv "),paste0(cancer.id,"/rnaseq_fpkm_*.csv")),intern=F)
sh: 1: gsutil: not found
Warning message:
In system(paste0("gsutil cp ", paste0(bucket, cancer.id, "/rnaseq_fpkm_*.csv "), :
error in running command
Any assistance would be greatly appreciated.
If you want to add to your path rather than replace, the withr::with_path gives a good short term solution. You can also use expand.path to expand user paths to full paths. Try
withr::with_path( path.expand("~/google-cloud-sdk/bin/"), {
system(paste0("gsutil cp ",paste0(bucket,cancer.id,"/rnaseq_fpkm_*.csv "),paste0(cancer.id,"/rnaseq_fpkm_*.csv")),intern=F)
})
Or even just to check that it works, try
withr::with_path( path.expand("~/google-cloud-sdk/bin/"), {
print(Sys.getenv("PATH"))
print(Sys.which("gsutil"))
})
In tensorflow the training from the scratch produced following 6 files:
events.out.tfevents.1503494436.06L7-BRM738
model.ckpt-22480.meta
checkpoint
model.ckpt-22480.data-00000-of-00001
model.ckpt-22480.index
graph.pbtxt
I would like to convert them (or only the needed ones) into one file graph.pb to be able to transfer it to my Android application.
I tried the script freeze_graph.py but it requires as an input already the input.pb file which I do not have. (I have only these 6 files mentioned before). How to proceed to get this one freezed_graph.pb file? I saw several threads but none was working for me.
You can use this simple script to do that. But you must specify the names of the output nodes.
import tensorflow as tf
meta_path = 'model.ckpt-22480.meta' # Your .meta file
output_node_names = ['output:0'] # Output nodes
with tf.Session() as sess:
# Restore the graph
saver = tf.train.import_meta_graph(meta_path)
# Load weights
saver.restore(sess,tf.train.latest_checkpoint('path/of/your/.meta/file'))
# Freeze the graph
frozen_graph_def = tf.graph_util.convert_variables_to_constants(
sess,
sess.graph_def,
output_node_names)
# Save the frozen graph
with open('output_graph.pb', 'wb') as f:
f.write(frozen_graph_def.SerializeToString())
If you don't know the name of the output node or nodes, there are two ways
You can explore the graph and find the name with Netron or with console summarize_graph utility.
You can use all the nodes as output ones as shown below.
output_node_names = [n.name for n in tf.get_default_graph().as_graph_def().node]
(Note that you have to put this line just before convert_variables_to_constants call.)
But I think it's unusual situation, because if you don't know the output node, you cannot use the graph actually.
As it may be helpful for others, I also answer here after the answer on github ;-).
I think you can try something like this (with the freeze_graph script in tensorflow/python/tools) :
python freeze_graph.py --input_graph=/path/to/graph.pbtxt --input_checkpoint=/path/to/model.ckpt-22480 --input_binary=false --output_graph=/path/to/frozen_graph.pb --output_node_names="the nodes that you want to output e.g. InceptionV3/Predictions/Reshape_1 for Inception V3 "
The important flag here is --input_binary=false as the file graph.pbtxt is in text format. I think it corresponds to the required graph.pb which is the equivalent in binary format.
Concerning the output_node_names, that's really confusing for me as I still have some problems on this part but you can use the summarize_graph script in tensorflow which can take the pb or the pbtxt as an input.
Regards,
Steph
I tried the freezed_graph.py script, but the output_node_name parameter is totally confusing. Job failed.
So I tried the other one: export_inference_graph.py.
And it worked as expected!
python -u /tfPath/models/object_detection/export_inference_graph.py \
--input_type=image_tensor \
--pipeline_config_path=/your/config/path/ssd_mobilenet_v1_pets.config \
--trained_checkpoint_prefix=/your/checkpoint/path/model.ckpt-50000 \
--output_directory=/output/path
The tensorflow installation package I used is from here:
https://github.com/tensorflow/models
First, use the following code to generate the graph.pb file.
with tf.Session() as sess:
# Restore the graph
_ = tf.train.import_meta_graph(args.input)
# save graph file
g = sess.graph
gdef = g.as_graph_def()
tf.train.write_graph(gdef, ".", args.output, True)
then, use summarize graph get the output node name.
Finally, use
python freeze_graph.py --input_graph=/path/to/graph.pbtxt --input_checkpoint=/path/to/model.ckpt-22480 --input_binary=false --output_graph=/path/to/frozen_graph.pb --output_node_names="the nodes that you want to output e.g. InceptionV3/Predictions/Reshape_1 for Inception V3 "
to generate the freeze graph.
I'm running lessc as following:
lessc alice/public/local/less/intfarm.less > alice/public/local/css/local/compiled/intfarm.css --source-map=alice/public/local/less/intfarm.map --verbose
the source map is output but it doesn't work. I check the file and at the end I read:
...
,iBAAA;EACA,cAAA;;AA1EZ,IAAI,SA8EA;EACI,gBAAA","file":"../../../../undefined
do I need to set other flags as well?
(shoutout at LESS creators: why not enable this by default and save us hours of work and searching?)
You should not use the > between your source and destiny. In fact your send the output to stdout. The compiler don't know that you are writing the output to intfarm.css and so can not construct the source map link to that file.
Also see: https://github.com/less/less.js/pull/2389
another solution can be using --source-map-map-inline parameter instead of --source-map=... but I think the best solution is the one pointed by Bass Jobsen