Once your account is activated, you can log in different ways.

 

  Terminal

ssh stage01@front.migale.inrae.fr

 

  Windows

For Windows, you need to use a terminal emulator tool such as MoBaXterm.

We regularly encounter problems with our LDAP. If your password doesn't work anymore (without any reason), the first reflex is to reset it, this solves a good part of the password problems. We are working on this problem.
You can reset it thanks to the dedicated form.

The only way to change your password is to fill the dedicated form.
If you lost your password, send a mail at help-migale@inra.fr. We will attribute you a new password and then you can change it easyly with the previous link.

Imagine you want to copy the file myfile.txt to the directory /projet/tmp/ on the migale server.

 

  Terminal

scp myfile.txt stage01@front.migale.inrae.fr:/projet/tmp/

The password will be asked.

 

For copying a directory, add the -r option after scp

scp -r mydir stage01@front.migale.inrae.fr:/projet/tmp/

 

  Windows

For Windows, you need to use a tool such as FileZilla.

stage01@front:~$ conda info --envs
# conda environments:
#
base                  *  /usr/local/genome/Anaconda2-5.1.0
BasicQC                  /usr/local/genome/Anaconda2-5.1.0/envs/BasicQC
abyss-2.2.1              /usr/local/genome/Anaconda2-5.1.0/envs/abyss-2.2.1
admixture-1.3.0          /usr/local/genome/Anaconda2-5.1.0/envs/admixture-1.3.0
amos-3.1.0               /usr/local/genome/Anaconda2-5.1.0/envs/amos-3.1.0
...

Imagine I want to know the name of the bwa conda environment. I can find it by typing:

stage01@front:~$ conda info --envs | grep bwa
bwa-0.7.17 /usr/local/genome/Anaconda2-5.1.0/envs/bwa-0.7.17

To use bwa with conda, you need to activate the bwa environment

stage01@front:~$ conda activate bwa-0.7.17
(bwa-0.7.17) stage01@front:~$ bwa

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li

Usage:   bwa command [options]

Command: index         index sequences in the FASTA format
mem           BWA-MEM algorithm
fastmap       identify super-maximal exact matches
pemerge       merge overlapping paired ends (EXPERIMENTAL)
aln           gapped/ungapped alignment
samse         generate alignment (single ended)
sampe         generate alignment (paired ended)
bwasw         BWA-SW for long queries

shm           manage indices in shared memory
fa2pac        convert FASTA to PAC format
pac2bwt       generate BWT from PAC
pac2bwtgen    alternative algorithm for generating BWT
bwtupdate     update .bwt to the new format
bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
There are three alignment algorithms in BWA: `mem', `bwasw', and
`aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
first. Please `man ./bwa.1' for the manual.

And to leave conda environment

stage01@front:~$ conda deactivate 
stage01@front:~$

To use a conda environment, it is necessary to tell snakemake to load the profile.d/conda.sh. To do this, add these lines at the beginning of your Snakefile:

shell.executable("/bin/bash")
shell.prefix("source /usr/local/genome/Anaconda3/etc/profile.d/conda.sh;")

In your snakemake rules, you can now use the conda environments with: conda activate my_env. As a reminder, the list of available environments is accessible with:

conda info --envs

Moreover, if you launch snakemake inside a shell script, you need add the following line at the beginning of your script:

source /usr/local/genome/Anaconda3/etc/profile.d/conda.sh

This is a minimal example for a rule that launches fastqc:

shell.executable("/bin/bash")
shell.prefix("source /usr/local/genome/Anaconda3/etc/profile.d/conda.sh;")

rule all:
	input:
		expand("qc/fastqc/{sample}_fastqc.html", sample = ["A", "B", "C"])

rule fastqc:
	input:
		"reads/{sample}.fastq.gz"
	output:
		html = "qc/fastqc/{sample}_fastqc.html",
		zip = "qc/fastqc/{sample}_fastqc.zip"
	params: "--quiet"
	log: "logs/fastqc/{sample}.log"
	threads: 1
	shell:
		"""
		conda activate fastqc-0.11.9
		fastqc {params} --threads {threads} --outdir qc/fastqc/ {input} > {log}
		conda deactivate
		"""

More information here in the Snakemake FAQ. If you obtain this error message:

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init 

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

check if you have a section called conda initialize in the file ~/.bashrc and remove it.

To use multiple threads, you have to specify it by adding -pe thread to your submission command.

Example:

stage01@front:~$ qsub -pe thread 8 myscript.sh

The Eqw state indicates that your job is in error state. To obtain the reason why, use the qstat command with your job-ID.

Example:

stage01@front:~$ qsub -cwd -V -N myblast -o /out/myblast.stdout -b y "blastn -db subject.fasta -query query.fasta -out /out/out.blast"
Your job 1995192 ("myblast") has been submitted
stage01@front:~$ qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
1995192 0.00000 myblast    stage01         Eqw    10/04/2019 17:11:46                                    1        

stage01@front:~$ qstat -j 1995192
...
error reason          1:      10/16/2019 14:35:39 [46342:142027]: error: can't open output file "/out/myblast.stdout": No such file or directory
...

stage01@front:~$ qstat
job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID 
-----------------------------------------------------------------------------------------------------------------
2039350 0.60500 myblast    stage01         qw    10/16/2019 14:44:34                                   100        

In some cases, jobs are never started and will never be started. In this example, the number of reserved threads is higher than what the nodes offer. As a result, SGE waits until it has a 100-slot node at its disposal to start your job. To check if the waiting is normal, use the qstat command with the job number to check that there is no warning as in this example. You will find here the detail about our resources.

stage01@front:~$ qstat -j 2039350
...
cannot run in PE "thread" because it only offers 0 slots
...

If you leave your session, you can be informed by mail when your jobs are finished using the specific options offered by SGE (command qsub):

• -m ea Will send email when job ends or aborts
• -M <emailaddress> Email address to send email to

If you keep working on front, you can use the command watch. Watch is used to run any arbitrary command at regular intervals and displays the output of the command on the terminal window. It is useful when you have to execute a command repeatedly and watch the command output change over time. In this case, the output of qstat will be empty.

stage01@front:~$ watch -n 5 "qstat"
# Will run qstat every 5 seconds

When you delete a dataset, it is not really deleted but hidden. It is a security in case of misuse. You can restore them. To delete them permanently, click on the button Delete permanently from disk. The quota will then be updated.

The most common reason why Galaxy cannot build a workflow from a history is that one of the tools used has been updated and parameters have changed. The only solution is to build a worflow from scratch.

If you get an error message by connecting to Galaxy's address such as Proxy Error or Service is unavailable or the navigation is very slow, contact us at help-migale@inrae.fr  Galaxy has probably crashed, we may need to restart it.

The "tar" command allows you to archive several files or the entire contents of a folder in a single file. The "z" parameter requires the tar file to becompressed so that it takes up  less disk space

Create tar.gz archive file

stage01@front:~$ tar cvzf archive_name.tar.gz folder_to_archive

Untar and uncompress tar.gz archive file

stage01@front:~$ tar xvfz archive_name.tar.gz

tar usage and options

• c create a archive file
• x extract a archive file
• v show the progress of archive file
• f filename of archive file
• t viewing content of archive file
• j filter archive through bzip2
• z filter archive through gzip

It means you have no space left on the directory you want to write. You need to check your quotas with command get_quota

stage01@front:~$ get_quota
Information for stage01 at mar. 01 févr. 2022 09:45:22 CET
Home  :  110.8MB  /  1GB    (11%)
Save  :  0B       /  50GB   (0%)
Work  :  8KB      /  150GB  (0%)

And to see details by folder you can use the du command

stage01@front:~$ du -sh ~/myfolder/*
1,7G	/home/stage01/myfolder/checkm-genome-1.0.18
8,0K	/home/stage01/myfolder/checkm_test
8,0K	/home/stage01/myfolder/checkm_test_results
4,0K	/home/stage01/myfolder/dir1
...

On migale, the path to perl was /usr/local/public/perl-5-24.0/bin/perl Now, the path to perl is /usr/bin/perl

stage01@front:~$ which perl
/usr/bin/perl

On migale, Python 2.7.13 was available and was the default version. Now, Python 3.8.10 is the default version.

stage01@front:~$ python --version
Python 3.8.10

Python 2 is no more maintained since end of 2019. We strongly recommand you to use Python3 if you begin a new project, or to upgrade your code to Python3. You can find details on what changed between the two versions.