LinuxQuestions.org - Want to allow disk space to /boot, or want to boot from other disk (16TB)

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Want to allow disk space to /boot, or want to boot from other disk (16TB)

Hi there,
I am new in Linux system. Here is my disk space details(attached). Whenever I want to login as user the system just doesn't give any response but I can login as root. It seems my /boot disk hasn't enough space. How can I allow disk space to the /boot (I have enough space in the 16TB disk). Is there any way that I can login through 16TB disk (/dev/sda1)?

[root@workstation01 ~]# df
Filesystem 1K-blocks Used Available Use% Mounted on
/dev/sdb2 112458088 12718008 99740080 12% /
devtmpfs 90639296 0 90639296 0% /dev
tmpfs 90648436 84 90648352 1% /dev/shm
tmpfs 90648436 9656 90638780 1% /run
tmpfs 90648436 0 90648436 0% /sys/fs/cgroup
/dev/sda1 15623790592 1750091440 13873699152 12% /mnt/831da725-3de4-46de-b6d4-30d15fd92d25
/dev/sdb1 508588 437880 70708 87% /boot
[root@workstation01 ~]#

Can you please provide a bit more information? For some reason you think that you don't have enough space in /boot and that this is somehow leading to your normal user not being able to log in. (I don't see how these two facts should be related, but I might be missing something.)

For people to be able to help it would help if you gave a bit of background info.
What distro are you using?
How are you trying to login? (Are you physically sitting in front of the computer or are you logging in remotely, e.g. through ssh? Are you logging in on a terminal or are you using a graphical login manager?)

You do have enough space in /boot, and even if you didn't that would have nothing at all to do with logging in as a regular user vs root. We need a lot more information as joe mentioned.

#
# /etc/fstab
# Created by anaconda on Fri Jul 24 12:08:27 2015
#
# Accessible filesystems, by reference, are maintained under '/dev/disk'
# See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
#
UUID=a7b150bf-f04a-4af0-917f-b9e8a6a45f35 / xfs defaults 1 1
UUID=d92c7e03-d559-48be-aaef-eb58b1608e6a /boot xfs defaults 1 2
/dev/sdb1 /home xfs defaults,usrquota,grpquota 1 2
UUID=bc6779ef-36cb-41ed-8f5d-21d2e7248b6b swap swap defaults 0 0
/dev/disk/by-uuid/831da725-3de4-46de-b6d4-30d15fd92d25 /mnt/831da725-3de4-46de-b6d4-30d15fd92d25 auto nosuid,nodev,nofail,x-gvfs-show 1 2

I am using the following system: Initially I had 64 Gb memory. Then I added extra memory. After added the memories I lost the GUI (maybe there was update issue with yum). Then I downloaded and installed "NVIDIA-Linux-x86_64-331.67.run". Now the GUI is working. But I can't login as a user in the desktop using my ID and password. But I can login through ssh using the same username and password. I also can login as root and I can access all of my files. But I don't want to login as root. I am new in the system administrator arena. Would you please to help me.

Best Regards
Zillur

System: Host: workstation01 Kernel: 3.10.0-229.14.1.el7.x86_64 x86_64 (64 bit gcc: 4.8.3)
Desktop: Gnome 3.8.4 Distro: CentOS Linux release 7.1.1503 (Core)
Machine: Mobo: ASUSTeK model: Z10PE-D16 WS v: Rev 1.xx
Bios: AmericaSystem: Host: workstation01 Kernel: 3.10.0-229.14.1.el7.x86_64 x86_64 (64 bit gcc: 4.8.3)
Desktop: Gnome 3.8.4 Distro: CentOS Linux release 7.1.1503 (Core)
Machine: Mobo: ASUSTeK model: Z10PE-D16 WS v: Rev 1.xx
Bios: American Megatrends v: 1001 date: 03/17/2015
CPU(s): 2 Octa core Intel Xeon E5-2630 v3s (-HT-MCP-SMP-) cache: 40960 KB
flags: (lm nx sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx) bmips: 76630
clock speeds: max: 3200 MHz 1: 1200 MHz 2: 1316 MHz 3: 1200 MHz
4: 1399 MHz 5: 1287 MHz 6: 1219 MHz 7: 1214 MHz 8: 1278 MHz
9: 1298 MHz 10: 1472 MHz 11: 1803 MHz 12: 1200 MHz 13: 1231 MHz
14: 1237 MHz 15: 1296 MHz 16: 1200 MHz
Graphics: Card: NVIDIA GK208 [GeForce GT 720] bus-ID: 81:00.0
Display Server: X.org 1.15.0 driver: nvidia
tty size: 80x24 Advanced Data: N/A for root
Audio: Card-1 NVIDIA GK208 HDMI/DP Audio Controller
driver: snd_hda_intel bus-ID: 81:00.1
Card-2 Intel C610/X99 series HD Audio Controller
driver: snd_hda_intel bus-ID: 00:1b.0
Sound: ALSA v: k3.10.0-229.14.1.el7.x86_64
Network: Card-1: Intel I210 Gigabit Network Connection
driver: igb v: 5.2.13-k port: 5000 bus-ID: 05:00.0
IF: eth0 state: down mac: <filter>
Card-2: Intel I210 Gigabit Network Connection
driver: igb v: 5.2.13-k port: 4000 bus-ID: 06:00.0
IF: eth1 state: up speed: 1000 Mbps duplex: full mac: <filter>
Drives: HDD Total Size: 16120.9GB (11.2 used)
ID-1: /dev/sda model: MR9361 size: 16000.9GB temp: 0C
ID-2: /dev/sdb model: INTEL_SSDSCKJW12 size: 120.0GB temp: 46C
Partition: ID-1: / size: System: Host: workstation01 Kernel: 3.10.0-229.14.1.el7.x86_64 x86_64 (64 bit gcc: 4.8.3)
Desktop: Gnome 3.8.4 Distro: CentOS Linux release 7.1.1503 (Core)
Machine: Mobo: ASUSTeK model: Z10PE-D16 WS v: Rev 1.xx
Bios: American Megatrends v: 1001 date: 03/17/2015
CPU(s): 2 Octa core Intel Xeon E5-2630 v3s (-HT-MCP-SMP-) cache: 40960 KB
flags: (lm nx sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx) bmips: 76630
clock speeds: max: 3200 MHz 1: 1200 MHz 2: 1316 MHz 3: 1200 MHz
4: 1399 MHz 5: 1287 MHz 6: 1219 MHz 7: 1214 MHz 8: 1278 MHz
9: 1298 MHz 10: 1472 MHz 11: 1803 MHz 12: 1200 MHz 13: 1231 MHz
14: 1237 MHz 15: 1296 MHz 16: 1200 MHz
Graphics: Card: NVIDIA GK208 [GeForce GT 720] bus-ID: 81:00.0
Display Server: X.org 1.15.0 driver: nvidia
tty size: 80x24 Advanced Data: N/A for root
Audio: Card-1 NVIDIA GK208 HDMI/DP Audio Controller
driver: snd_hda_intel bus-ID: 81:00.1
Card-2 Intel C610/X99 series HD Audio Controller
driver: snd_hda_intel bus-ID: 00:1b.0
Sound: ALSA v: k3.10.0-229.14.1.el7.x86_64
Network: Card-1: Intel I210 Gigabit Network Connection
driver: igb v: 5.2.13-k port: 5000 bus-ID: 05:00.0
IF: eth0 state: down mac: <filter>
Card-2: Intel I210 Gigabit Network Connection
driver: igb v: 5.2.13-k port: 4000 bus-ID: 06:00.0
IF: eth1 state: up speed: 1000 Mbps duplex: full mac: <filter>
Drives: HDD Total Size: 16120.9GB (11.2% used)
ID-1: /dev/sda model: MR9361 size: 16000.9GB temp: 0C
ID-2: /dev/sdb model: INTEL_SSDSCKJW12 size: 120.0GB temp: 46C
Partition: ID-1: / size: 108G used: 6.7G (7%) fs: xfs dev: /dev/sdb2
ID-2: /boot size: 497M used: 251M (51%) fs: xfs dev: /dev/sdb1
ID-3: swap-1 size: 4.29GB used: 0.00GB (0%) fs: swap dev: /dev/sdb3
RAID: No RAID devices: /proc/mdstat, md_mod kernel module present
Sensors: System Temperatures: cpu: 36.0C mobo: N/A gpu: 0.0:47C
Fan Speeds (in rpm): cpu: N/A
Info: Processes: 318 Uptime: 3 days Memory: 2550.2/177047.7MB
Init: systemd runlevel: 5 Gcc sys: 4.8.3
Client: Shell (bash 4.2.461) inxi: 2.2.28 108G used: 6.7G (7%) fs: xfs dev: /dev/sdb2
ID-2: /boot size: 497M used: 251M (51%) fs: xfs dev: /dev/sdb1
ID-3: swap-1 size: 4.29GB used: 0.00GB (0%) fs: swap dev: /dev/sdb3
RAID: No RAID devices: /proc/mdstat, md_mod kernel module present
Sensors: System Temperatures: cpu: 36.0C mobo: N/A gpu: 0.0:47C
Fan Speeds (in rpm): cpu: N/A
Info: Processes: 318 Uptime: 3 days Memory: 2550.2/177047.7MB
Init: systemd runlevel: 5 Gcc sys: 4.8.3
Client: Shell (bash 4.2.461) inxi: 2.2.28 n Megatrends v: 1001 date: 03/17/2015
CPU(s): 2 Octa core Intel Xeon E5-2630 v3s (-HT-MCP-SMP-) cache: 40960 KB
flags: (lm nx sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx) bmips: 76630
clock speeds: max: 3200 MHz 1: 1200 MHz 2: 1316 MHz 3: 1200 MHz
4: 1399 MHz 5: 1287 MHz 6: 1219 MHz 7: 1214 MHz 8: 1278 MHz
9: 1298 MHz 10: 1472 MHz 11: 1803 MHz 12: 1200 MHz 13: 1231 MHz
14: 1237 MHz 15: 1296 MHz 16: 1200 MHz
Graphics: Card: NVIDIA GK208 [GeForce GT 720] bus-ID: 81:00.0
Display Server: X.org 1.15.0 driver: nvidia
tty size: 80x24 Advanced Data: N/A for root
Audio: Card-1 NVIDIA GK208 HDMI/DP Audio Controller
driver: snd_hda_intel bus-ID: 81:00.1
Card-2 Intel C610/X99 series HD Audio Controller
driver: snd_hda_intel bus-ID: 00:1b.0
Sound: ALSA v: k3.10.0-229.14.1.el7.x86_64
Network: Card-1: Intel I210 Gigabit Network Connection
driver: igb v: 5.2.13-k port: 5000 bus-ID: 05:00.0
IF: eth0 state: down mac: <filter>
Card-2: Intel I210 Gigabit Network Connection
driver: igb v: 5.2.13-k port: 4000 bus-ID: 06:00.0
IF: eth1 state: up speed: 1000 Mbps duplex: full mac: <filter>
Drives: HDD Total Size: 16120.9GB (11.2% used)
ID-1: /dev/sda model: MR9361 size: 16000.9GB temp: 0C
ID-2: /dev/sdb model: INTEL_SSDSCKJW12 size: 120.0GB temp: 46C
Partition: ID-1: / size: 108G used: 6.7G (7%) fs: xfs dev: /dev/sdb2
ID-2: /boot size: 497M used: 251M (51%) fs: xfs dev: /dev/sdb1
ID-3: swap-1 size: 4.29GB used: 0.00GB (0%) fs: swap dev: /dev/sdb3
RAID: No RAID devices: /proc/mdstat, md_mod kernel module present
Sensors: System Temperatures: cpu: 36.0C mobo: N/A gpu: 0.0:47C
Fan Speeds (in rpm): cpu: N/A
Info: Processes: 318 Uptime: 3 days Memory: 2550.2/177047.7MB
Init: systemd runlevel: 5 Gcc sys: 4.8.3
Client: Shell (bash 4.2.461) inxi: 2.2.28

scrap that, misread your post

here is the 16tb disk.

I am trying to login directly, not remotely.

Why are you trying to mount /dev/sdb1 to /home in your fstab? sdb1 is a 500M boot partition, it should NOT be mounted at /home. Unless you have a good reason for doing that, which I highly doubt, delete that line from your fstab.

Probably your user is no member of video group ... just guessing.

/dev/sdb1 /home xfs defaults,usrquota,grpquota 1 2

So, I just need to delete this 3rd line only from /etc/fstab? And anything I need to do?

I want to mount /dev/sda1 as /home. But don't know how? Would you please to help me.

Quote:

Originally Posted by Emerson (Post 5440620)

Probably your user is no member of video group ... just guessing.

what is a video group? How can I include my user in this group?

What is confusing is that the output of the df command shows /sdb1 as /boot but the attached image and your /etc/fstab file show that sdb1 is also mounted as /home. If your /home is also on your /boot partition then that could be the reason why you can not login because your also using quotas and it is only 524MB.

Post the output of the command blkid. This will show all of your filesystems information i.e. partition, file system type and UUID.

[root@workstation01 ~]# blkid
/dev/sda1: UUID="831da725-3de4-46de-b6d4-30d15fd92d25" TYPE="xfs" PARTLABEL="workstation" PARTUUID="3e643245-60a6-4100-b807-0f4145e6c9ee"
/dev/sdb1: LABEL="BOOT" UUID="d92c7e03-d559-48be-aaef-eb58b1608e6a" TYPE="xfs"
/dev/sdb2: LABEL="ROOT" UUID="a7b150bf-f04a-4af0-917f-b9e8a6a45f35" TYPE="xfs"
/dev/sdb3: LABEL="SWAP1" UUID="bc6779ef-36cb-41ed-8f5d-21d2e7248b6b" TYPE="swap"

Quote:

Originally Posted by zillur (Post 5440622)

Yes absolutely remove that line and see if it fixes your problem. Once your system is functional, we can go through migrating /home onto your 16 TB array, I've done it many times.

Quote:

So, I just need to delete this 3rd line only from /etc/fstab? And anything I need to do?

Yes, then reboot. Or you could comment the line out by putting a hash mark at the beginning of the line as shown below and rebooting. You could then put a comment on a line above it explaining the problem and why it should not be done for future reference.

Quote:

#/dev/sdb1 /home xfs defaults,usrquota,grpquota 1 2

As pointed out above, you have boot and home mounted to the same partition but it is actually just the boot partition. You have a home mount point in fstab of sdb1 and if you look at the blkid output, the uuid for boot is sdb1. That will be nothing but problems.

If what you are trying to do is get home mounted as a separate partition on sda1, the simplest way to do that is to create a separate partition for it during install. You could create a mount point for sda1 now then create a proper entry for it in fstab and copy the home directory and its contents there. Since I've only done that once, I'll leave it to others to explain how to do it.

Thank you all for your valuable suggestions. I changed my /etc/fstab file, like this. But the problem is not solved. Waiting for your comments.....

#
# /etc/fstab
# Created by anaconda on Fri Jul 24 12:08:27 2015
#
# Accessible filesystems, by reference, are maintained under '/dev/disk'
# See man pages fstab(5), findfs(8), mount(8) and/or blkid(8) for more info
#
UUID=a7b150bf-f04a-4af0-917f-b9e8a6a45f35 / xfs defaults 1 1
UUID=d92c7e03-d559-48be-aaef-eb58b1608e6a /boot xfs defaults 1 2
#/dev/sdb1 /home xfs defaults,usrquota,grpquota 1 2
UUID=bc6779ef-36cb-41ed-8f5d-21d2e7248b6b swap swap defaults 0 0
/dev/disk/by-uuid/831da725-3de4-46de-b6d4-30d15fd92d25 /mnt/831da725-3de4-46de-b6d4-30d15fd92d25 auto nosuid,nodev,nofail,x-gvfs-show 1 2

When you changed /etc/fstab /home is now on the / drive (sdb2) which may or may not be empty but now whatever was in your users home directories does not show up under /home/ anymore. What is currently on sda1 (/mnt/831da725-3de4-46de-b6d4-30d15fd92d25) and what is its purpose?

Thanks a lot. This is my hard disk(16 TB) and all my data and tools in this disk. I want to mount /sda1 as /home.

Please reboot the system, log in as root, and post the contents of /boot and /home.

Also, when you're logged in as root, what happens if you open a terminal and run "su - user", where user is the username you are trying to log in as and failing.

I can go to any user using su user. but there is nothing without a user "act" this user was created at the very beginning.

[root@workstation01 ~]# cd /boot
[root@workstation01 boot]# ls
config-3.10.0-229.11.1.el7.x86_64
config-3.10.0-229.14.1.el7.x86_64
config-3.10.0-229.7.2.el7.x86_64
config-3.10.0-229.el7.x86_64
extlinux
grub
grub2
initramfs-0-rescue-0f1e31e901a7431887b53be42b60a009.img
initramfs-3.10.0-229.11.1.el7.x86_64.img
initramfs-3.10.0-229.11.1.el7.x86_64kdump.img
initramfs-3.10.0-229.14.1.el7.x86_64.img
initramfs-3.10.0-229.14.1.el7.x86_64.img.backup
initramfs-3.10.0-229.14.1.el7.x86_64kdump.img
initramfs-3.10.0-229.7.2.el7.x86_64.img
initramfs-3.10.0-229.7.2.el7.x86_64kdump.img
initramfs-3.10.0-229.7.2.el7.x86_64-nouveau.img
initramfs-3.10.0-229.el7.x86_64.img
initramfs-3.10.0-229.el7.x86_64kdump.img
initrd-plymouth.img
nvidia.tx
shulav
symvers-3.10.0-229.11.1.el7.x86_64.gz
symvers-3.10.0-229.14.1.el7.x86_64.gz
symvers-3.10.0-229.7.2.el7.x86_64.gz
symvers-3.10.0-229.el7.x86_64.gz
System.map-3.10.0-229.11.1.el7.x86_64
System.map-3.10.0-229.14.1.el7.x86_64
System.map-3.10.0-229.7.2.el7.x86_64
System.map-3.10.0-229.el7.x86_64
vmlinuz-0-rescue-0f1e31e901a7431887b53be42b60a009
vmlinuz-3.10.0-229.11.1.el7.x86_64
vmlinuz-3.10.0-229.14.1.el7.x86_64
vmlinuz-3.10.0-229.7.2.el7.x86_64
vmlinuz-3.10.0-229.el7.x86_64
[root@workstation01 boot]# cd /home/
[root@workstation01 home]# ls
act
[root@workstation01 home]# su zillur
bash-4.2$ ls
act
bash-4.2$ su shulav
Password:
bash-4.2$ ls
act
bash-4.2$

Looks like you have a weird combination of home directories in both locations.

act has a directory in /home, and shulav has a directory in /boot, but those are the only ones I see. How was the user "zillur" created? How many users do you have? What happens if you try to su to act? Also, you should be using "su - user" as I provided in my example, not "su user".

To start with you should move shulav from /boot to /home. I don't see anything else in /boot that doesn't belong.

Which user are you trying to log in as on the GUI when it hangs?

Thank you very much.I can login as "act" and "root". After login as "act" now how can I fix all these problems?

First move shulav from /boot to /home. We also need to figure out what happened to zillur's home directory since it's not in either location, as well as any other users you've created on the system.

Once everything that needs to be in /home has been moved to /home, you need to log out as all regular users and log in as root (either on the GUI or a TTY, I prefer the TTY since I don't like logging in as root on the GUI). Use "w" to verify no other users are logged in, and also make sure sda1 is mounted at /mnt/831da725-3de4-46de-b6d4-30d15fd92d25. Then then run the following:

Code:

cp -a /home/* /mnt/831da725-3de4-46de-b6d4-30d15fd92d25/

mv /home /home.backup

umount /mnt/831da725-3de4-46de-b6d4-30d15fd92d25

mkdir /home

mount /dev/sda1 /home

Then log out as root and log in as your regular user again, verify everything works and looks as expected. Once you're sure it looks right, add the new mount to /etc/fstab:

Code:

UUID=831da725-3de4-46de-b6d4-30d15fd92d25 /home xfs defaults 1 2

and remove the old line that was mounting it in /mnt, and reboot.

Once you're sure everything is correct, you can remove /home.backup

By mounting sda1 on /home the OP will still have still have a messy combination of data and tools in the /home directory. IMHO it would be best to separate them...

I agree, but that's where he said he wanted it mounted, so that's what I went with. It would also be possible to mount sda1 elsewhere and create a directory inside of it for all of the users' home directories, then bind mount that to /home, or change the default home directory for all users from /home to this new location. Lots of options.

Yep. lots of options.

Thank you all for your valuable suggestions. Now I can login as any user. I have another question. I installed some tools in "/home/zillur/Desktop/zillur/Tools" this folder. like:
bcftools-1.2
bcftools-1.2.tar.bz2
bowtie2-2.2.5
bowtie2-2.2.5-linux-x86_64.zip
epel-release-latest-7.noarch.rpm
fastqc
GenomeAnalysisTK-3.4-46.tar.bz2
etc.
I can run them as user "zillur"
I want to allow my other users to run this tools. How can I do this?

Best Regards
Zillur

You need to place them somewhere neutral, where all users have access. A common location is /usr/local/

Thank you very much. I have moved this folder to /usr/local. Then what I need to do? after moving this: /usr/local/Tools, my tools are not working. Like:
[zillur@workstation01 Tools]$ bowtie2
bash: bowtie2: command not found...
Maybe I am missing something.
Best Regards
Zillur

You'll need to add /usr/local/Tools to your PATH. To make it permanent make this change in one of your startup scripts, like .bashrc or .bash_profile, or the startup script for whatever shell you use, eg:

Code:

echo 'export PATH=$PATH:/usr/local/Tools' >> ~/.bashrc

Then either source .bashrc, or log out and back in, or open a new terminal, etc.

Thank you very much for your kind help. I have moved my "Tools" to /usr/local and edit my bash_profile. like this:
GNU nano 2.3.1 File: /home/zillur/.bash_profile

# .bash_profile

# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

# User specific environment and startup programs

PATH=$PATH:$HOME/.local/bin:$HOME/bin:/home/zillur/Desktop/zillur/Tools/bcftools-1.2:/usr/local/Tools/bowtie2-2.2.5:/home/zillur/Desktop/zillur/Tools/samtool$

export PATH

But its not working. Maybe I am missing something.
Best Regards
Zillur

[zillur@workstation01 Tools]$ cd bowtie2-2.2.5/
[zillur@workstation01 bowtie2-2.2.5]$ ls
AUTHORS bowtie2-align-s bowtie2-build-l bowtie2-inspect bowtie2-inspect-s-debug MANUAL TUTORIAL
bowtie2 bowtie2-align-s-debug bowtie2-build-l-debug bowtie2-inspect-l doc MANUAL.markdown VERSION
bowtie2-align-l bowtie2-build bowtie2-build-s bowtie2-inspect-l-debug example NEWS
bowtie2-align-l-debug bowtie2-buildc bowtie2-build-s-debug bowtie2-inspect-s LICENSE scripts
[zillur@workstation01 bowtie2-2.2.5]$ pwd
/usr/local/Tools/bowtie2-2.2.5
[zillur@workstation01 bowtie2-2.2.5]$ bowtie2
bash: bowtie2: command not found...
[zillur@workstation01 bowtie2-2.2.5]$

1. Please use CODE tags when posting; its hard to read otherwise
https://www.linuxquestions.org/quest...do=bbcode#code

2.

Code:

$HOME/.local/bin    # is the 'local' dir really hidden (leading 'dot' )



/home/zillur/Desktop/zillur/Tools/samtool$      # why is there a trailing '$' here

3. Have you set executable perms on that (I assume) binary?

Did you log out and back in or source the .bash_profile file after making the change?

Thank you very much for your kind reply. After log out and then log in it is working perfectly for me. But I want to allow other users to use these tools. How can I do this?
Best Regards
Zillur

They need to add /usr/local/Tools to their PATH as well, and you need to ensure that "other" read and execute permission is set on the directories and binaries in /usr/local/Tools.

Thank you very much for your kind suggestions. I have used other systems as a user(not as a administrator). That time I didn't need to add my PATH. Is there any way like this?
Best Regards
Zillur

You can print out the default PATH for a new user, and then symlink the binaries from their current location into one of the directories that's already in the PATH (eg: /usr/local/bin).

Quote:

Originally Posted by suicidaleggroll (Post 5443712)

You can print out the default PATH for a new user, and then symlink the binaries from their current location into one of the directories that's already in the PATH (eg: /usr/local/bin).

Thanks a lot for your suggestions. How can I print out the default PATH for a user and then how can I symlink? Sorry for bothering. I am new in this system.
Best Regards
Zillur

echo $PATH

Another method would be to create a script in your /etc/profile.d to add a global path for all users.

Code:

touch /etc/profile.d/custom.sh

chmod +x /etc/profile.d/custom.sh



Create the custom.sh script using any text editor.

#!/bin/sh

 

PATH=$PATH:/usr/local/Tools

export PATH

Thank you very much for your kind reply. I tried this. But it gave me a unusual error.

[gary@workstation01 ~]$ bowtie2
(ERR): Expected bowtie2 to be in same directory with bowtie2-align:
/usr/local/Tools/bowtie2-2.2.5/
Exiting now ...
[gary@workstation01 ~]$ cd /usr/local/Tools/bowtie2-2.2.5/
[gary@workstation01 bowtie2-2.2.5]$ ls
AUTHORS bowtie2-build-l-debug example
bowtie2 bowtie2-build-s LICENSE
bowtie2-align-l bowtie2-build-s-debug MANUAL
bowtie2-align-l-debug bowtie2-inspect MANUAL.markdown
bowtie2-align-s bowtie2-inspect-l NEWS
bowtie2-align-s-debug bowtie2-inspect-l-debug scripts
bowtie2-build bowtie2-inspect-s TUTORIAL
bowtie2-buildc bowtie2-inspect-s-debug VERSION
bowtie2-build-l doc
[gary@workstation01 bowtie2-2.2.5]$

Looks like you can't just symlink the executable because it has helper routines that need to be in the same directory. You'd either have to symlink all of them into your new location, or do as michaelk suggested and make the .profile changes universal by editing the system-wide initialization scripts.

Quote:

Originally Posted by suicidaleggroll (Post 5444186)

Thanks a lot. I have tried exactly like "michaelk" suggestion.

GNU nano 2.3.1 File: /etc/profile.d/custom.sh

#!/bin/sh

PATH=$PATH:/usr/local/Tools/bowtie2-2.2.5
export PATH

But.....

Quote:

Originally Posted by suicidaleggroll (Post 5444186)

Thanks a lot. But how can I do the "symlink"?

Quote:

Originally Posted by michaelk (Post 5443769)

echo $PATH

Another method would be to create a script in your /etc/profile.d to add a global path for all users.

Code:

touch /etc/profile.d/custom.sh

chmod +x /etc/profile.d/custom.sh



Create the custom.sh script using any text editor.

#!/bin/sh

 

PATH=$PATH:/usr/local/Tools

export PATH

Thanks a lot. I have done this but it's not working for my users. Any idea?

Thank you very much to all for helping me with your valuable suggestions. It's ok now. I had to give permission for all the executables. like:

Quote:

sudo chmod 755 /usr/local/folder/executable

That's it.

Best Regards
Zillur