Problems to install LTR_retriever

Dear Dr. Ou

I'm trying to install LTR_retriever on my computer, but I'm having no susses. I have Linux Ubuntu 20.04.

I run the following script: conda install -y -c bioconda cd-hit repeatmasker

And this is the answer: Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with a past explicit spec that is not an explicit spec in this operation (perl-text-soundex):

repeatmasker -> perl-text-soundex
repeatmasker -> perl[version='5.22.0.*|>=5.26.2,<5.26.3.0a0']
repeatmasker -> rmblast -> perl

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package _openmp_mutex conflicts for: cd-hit -> libgcc-ng[version='>=9.3.0'] -> _openmp_mutex[version='>=4.5'] _openmp_mutex perl -> libgcc-ng[version='>=7.5.0'] -> _openmp_mutex[version='>=4.5']

Package _libgcc_mutex conflicts for: cd-hit -> libgcc-ng[version='>=9.3.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge'] _libgcc_mutex libgomp -> _libgcc_mutex==0.1=conda_forge _openmp_mutex -> _libgcc_mutex==0.1[build='main|conda_forge'] perl -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='|0.1',build='main|conda_forge']

Package libgomp conflicts for: _openmp_mutex -> libgomp[version='>=7.5.0'] libgomp

Package libstdcxx-ng conflicts for: cd-hit -> libgcc -> libstdcxx-ng[version='>=7.2.0'] cd-hit -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=9.3.0']

Package perl conflicts for: perl perl-text-soundex -> perl[version='>=5.26.2,<5.26.3.0a0']

Package libgcc-ng conflicts for: cd-hit -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0'] repeatmasker -> h5py -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0|>=9.3.0|>=7.5.0'] perl -> libgcc-ng[version='>=7.2.0|>=7.5.0'] libgcc-ng cd-hit -> libgcc-ng[version='>=4.9|>=7.3.0|>=9.3.0'] perl-text-soundex -> perl[version='>=5.26.2,<5.26.3.0a0'] -> libgcc-ng[version='>=7.2.0|>=7.5.0']

Package libgcc conflicts for: cd-hit -> libgcc repeatmasker -> rmblast -> libgcc

I tried to solve some of the problems, trying to download the different lib independently, but no success.

Could you help me?

Thank you very much, and regards from Argentina, Rosalia

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-809936560, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATOO5BVPKFI3IRVEQPFSZP3TGFSTPANCNFSM42AGKI4Q .

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

There is a typo in your command, should be bioconda.

On Tue, Mar 30, 2021 at 10:02 PM rosaliapaz @.***> wrote:

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-809936560 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ATOO5BVPKFI3IRVEQPFSZP3TGFSTPANCNFSM42AGKI4Q

.

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-810280709, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NFLKOJXFIOBMWZMPULTGHKXFANCNFSM42AGKI4Q .

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Tue, Mar 30, 2021 at 11:01 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-809936560, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATOO5BVPKFI3IRVEQPFSZP3TGFSTPANCNFSM42AGKI4Q .

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Wed, Mar 31, 2021 at 10:49 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Tue, Mar 30, 2021 at 11:01 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-809936560, or unsubscribe https://github.com/notifications/unsubscribe-auth/ATOO5BVPKFI3IRVEQPFSZP3TGFSTPANCNFSM42AGKI4Q .

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

Sorry for the late reply. You may need to update conda to the Python 3 version.

Best, Shujun

On Tue, Apr 6, 2021 at 2:09 AM rosaliapaz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Wed, Mar 31, 2021 at 10:49 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Tue, Mar 30, 2021 at 11:01 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-809936560 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ATOO5BVPKFI3IRVEQPFSZP3TGFSTPANCNFSM42AGKI4Q

.

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-813549272, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NBLCET7WVOGQS343PLTHH4HNANCNFSM42AGKI4Q .

Dear Dr. Ou

Thank you for your answer. I ve installed python 3.9 and tried to run the command, and this was the answer:

(base) @.***:~$ conda install -y -c bioconda cd-hit repeatmasker Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for: cd-hit -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0'] repeatmasker -> h5py -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0|>=9.3.0|>=7.5.0'] python=3.8 -> libgcc-ng[version='>=7.3.0'] python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0'] cd-hit -> libgcc-ng[version='>=4.9|>=7.3.0|>=9.3.0']

Package _libgcc_mutex conflicts for: python=3.8 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] cd-hit -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]

Package libgcc conflicts for: cd-hit -> libgcc repeatmasker -> rmblast -> libgcc

:-(

Thanks for any help

On Mon, Apr 5, 2021 at 10:04 PM Shujun Ou @.***> wrote:

Sorry for the late reply. You may need to update conda to the Python 3 version.

Best, Shujun

On Tue, Apr 6, 2021 at 2:09 AM rosaliapaz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Wed, Mar 31, 2021 at 10:49 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Tue, Mar 30, 2021 at 11:01 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <

https://github.com/oushujun/LTR_retriever/issues/90#issuecomment-809936560

,

or unsubscribe <

https://github.com/notifications/unsubscribe-auth/ATOO5BVPKFI3IRVEQPFSZP3TGFSTPANCNFSM42AGKI4Q

.

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 < https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g

(Oeste), J5402DCS, Rivadavia

San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 < https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g

(Oeste), J5402DCS, Rivadavia

San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 < https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g

(Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

— You are receiving this because you commented.

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-- Dra. M.Sc. Rosalía C. Paz

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"Nada grande se puede hacer sin alegría"

-Jauretche-

You may have a conflict of using Python 3.8. Try to add python=3.7 in your conda command. Have you tried conda install -c bioconda ltr_retriever?

On Tue, Apr 6, 2021 at 9:54 PM rosaliapaz @.***> wrote:

Dear Dr. Ou

Thank you for your answer. I ve installed python 3.9 and tried to run the command, and this was the answer:

(base) @.***:~$ conda install -y -c bioconda cd-hit repeatmasker Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: | Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgcc-ng conflicts for: cd-hit -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0'] repeatmasker -> h5py -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0|>=9.3.0|>=7.5.0'] python=3.8 -> libgcc-ng[version='>=7.3.0'] python=3.8 -> zlib[version='>=1.2.11,<1.3.0a0'] -> libgcc-ng[version='>=7.2.0'] cd-hit -> libgcc-ng[version='>=4.9|>=7.3.0|>=9.3.0']

Package _libgcc_mutex conflicts for: python=3.8 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main] cd-hit -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex=[build=main]

Package libgcc conflicts for: cd-hit -> libgcc repeatmasker -> rmblast -> libgcc

:-(

Thanks for any help

On Mon, Apr 5, 2021 at 10:04 PM Shujun Ou @.***> wrote:

Sorry for the late reply. You may need to update conda to the Python 3 version.

Best, Shujun

On Tue, Apr 6, 2021 at 2:09 AM rosaliapaz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Wed, Mar 31, 2021 at 10:49 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Sorry for the typo mistake. Here I run it again, and this was the result:

(LTR_retriever) @.***:~$ conda install -c bioconda ltr_retriever Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: - Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

:-(

Thank you for any help. Regards from Argentina, Rosalia

On Tue, Mar 30, 2021 at 11:01 AM rosalia paz @.***> wrote:

Dear Dr. Ou

Thank you very much for your answer. Ive just tried to run the commands you send me, and the two first run ok, but the third gives me an error. Apparently, there is a channel change that is not recognized.

Thank you for any help. Regards from Argentina, rosalia

(LTR_retriever) @.***:~$ conda install -c biconda ltr_retriever Collecting package metadata (current_repodata.json): failed

UnavailableInvalidChannel: The channel is not accessible or is invalid. channel name: biconda channel url: https://conda.anaconda.org/biconda error code: 404

You will need to adjust your conda configuration to proceed. Use conda config --show channels to view your configuration's current state, and use conda config --show-sources to view config file locations.

On Tue, Mar 30, 2021 at 3:03 AM Shujun Ou @.***> wrote:

Hello Rosalia,

There is a conda recipe for LTR_retriever: https://anaconda.org/bioconda/ltr_retriever

Seems like your conda env has conflicts when installing dependencies. You may want to create a new env for LTR_retriever. i.e., conda create -n LTR_retriever, then conda activate LTR_retriever and conda install -c bioconda ltr_retriever.

Let me know if you still have issues.

Best, Shujun

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-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g <

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"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g <

https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g

(Oeste), J5402DCS, Rivadavia

San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

-- Dra. M.Sc. Rosalía C. Paz

Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g <

https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g

(Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

-Jauretche-

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Investigadora CONICET CIGEOBIO (FCEFyN, UNSJ/CONICET) Dpto. de Biología. Av. Ignacio de la Roza 590 https://www.google.com/maps/search/Av.+Ignacio+de+la+Roza+590?entry=gmail&source=g (Oeste), J5402DCS, Rivadavia San Juan, Argentina Te invito a que visites mi página web www.rosaliapaz.com http://rosaliapaz.com/

"Tú debes ser el cambio que quieres ver en el mundo" -Mahatma Gandhi-

"Nada grande se puede hacer sin alegría"

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Hi @rosaliapaz,

It has been a while, have you figured it out? Your last post showed that you were using the base env to install LTR_retriever. You should use a dedicated env to do so as I suggested in the initial response: conda create -n LTR_retriever python=3.7 conda activate LTR_retriever conda install -c bioconda ltr_retriever

Let me know if you have more issues.

Shujun

oushujun / LTR_retriever

Problems to install LTR_retriever #90